JONATHAN Mills's decision to ignore the independence referendum in next year's Edinburgh International Festival (EIF) has evoked two reactions: "Thank God" and "What on Earth is the EIF director thinking about?"

Some find it extraordinary that the biggest democratic and political challenge to the UK should be missing from Scotland's most prestigious cultural showcase, which in 2014 will finish just a couple of weeks before the big vote on September 18.

Others cannot visualise "independence-related productions" free of sentimentality or tub-thumping propaganda.

Yet the same dangers of cliche and bias face artists working on Commonwealth Games and First World War themes, which will be covered in the programme. Is it really so hard for artists to discuss universal themes through the prism of a real moment of choice that involves every Scottish adult (and may indirectly affect all UK citizens)?

The directors of the Book Festival and the National Theatre of Scotland (NTS) have embraced the referendum with relish (and commissions). So the problem for the EIF hardly appears to be artistic - it's political. Essentially, the independence referendum is not a British event - it's "only" Scottish. And the Edinburgh International Festival exists to explore Britain's changing place in the world, not the changing nature of places within Britain.

Scotland has been a physical backdrop at the Edinburgh International Festival for almost 70 years but has rarely enjoyed a starring role. One year from a potentially democracy-changing vote, that's not good enough. Big democratic issues about governance are clearly not "little local difficulties" any more - at least not to Scots.

And yet never mind independence. It's hard to imagine any event important only to Scots which might merit a place in the EIF's programme. This cultural predicament is explored in my new book, Blossom: What Scotland Needs To Flourish - and its roots go back a long way. When the independent Scottish state was formally dissolved in the Treaty Of Union, our culture became the chief standard-bearer of Scottish identity just as a large injection of British thinking was added to Scottish life - especially to the lives of the elite.

Crackdowns, clearance and emigration after Culloden removed Gaelic and Scots speakers along with their songs, outlooks, traditional instruments and folk customs. British cultural values became the safest to espouse and highbrow English traditions the most profitable to learn. Yet Scotland's native traditions somehow survived to be revered, adapted, neglected, forgotten, misrepresented and rediscovered all over again.

But in this bubbling mix one thing has been constant - the power wielded by funders, civil servants and arts administrators over what to show and what to store, what to expose to a Scotland-wide audience, what to confine to "experimental spaces" and what to simply ignore. There are just too many artefacts, traditions and distinct cultures to fit into the pint pots of funding streams, exhibition space, official events or time in the school curriculum. There is no way to avoid choice. And choice is a political act.

I began choosing early, "correcting" history books at school which seemed to confuse Britain, England and the UK. Despite the neatness of my work I was suspended. Lucky to sample the incredible wealth of Scottish song, poetry, writing, painting, sculpture and architecture early in life, I was baffled then infuriated to see how few artists could make a living, let alone a mark, on mainstream Scottish consciousness - no matter how sought-after outside Scotland. Opportunities to reach beyond "specialist" audiences, or receive more than travel expenses here, were extremely limited, even for giants in their own fields. When the renowned Shetland fiddler Tom Johnson died in 1991, I was in Ireland and watched a one-hour tribute programme on RTE. Back home on BBC Scotland, I found nothing.

Mercifully, thanks to the explosion of book festivals, traditional music events such as Celtic Connections, volunteer learning projects like the Gaelic Feisean, and the internationally acclaimed NTS - all established after years of lobbying by artists - the situation is now better. Scotland still isn't Ireland, where artists effectively live tax-free. But Scottish artists are taken more seriously - especially when they manage to dislodge directors of Creative Scotland.

And yet the dilemma remains. Which artist to choose? What performance to fund? And who should decide? Last year, Alasdair Gray hit the headlines after protesting about the high number of non-Scots in top arts jobs making these important judgment calls. He was particularly critical of folk who come and go without getting Scotland under their fingernails. All hell was let loose online and one of Alasdair's "colonists", Vicky Featherstone, wrote about feeling bullied because of her English origins when she became the first director of the NTS. It all got very personal, very fast.

Then last week, Gray defended his argument, saying "the Scots bodies that appoint heads are Scotophobic when it comes to their own kind". The terms employed by Gray are definitely loaded. "Settler" has the ugly connection of "white settler", "colonist" has the unattractive overtone of colonialism and phobic speaks for itself. But there is always a choice. People can react to Alasdair's terminology - or focus on the crucial subject he has raised. Is there a disproportionate number of non-Scots in top jobs, particularly in culture and the environment?

It seems strange that merely asking the question prompted immediate cries of anti-English racism. Most nations monitor the distribution of benefit - it's the only way to counter elitism and understand the impact of public policy. Only the very perverse would ascribe sexist motives to those who thought most speakers at the Yes Campaign launch were male. It was patently true. But cultural outlook is harder to define.

This is where Gary: Tank Commander comes in - a BBC Scotland sitcom in which a bunch of soldiers pass time in a Glasgow barracks, waiting to do combat in defence of Queen and country. In one episode, the eponymous hero holds up a small orange and asks if it's a clementine, tangerine or satsuma. "Naw," he concludes. "It's jist a wee orange - they're all wee oranges."

Now, this either prompts a laugh or you don't get it. Scots don't see much value in learning the tiny differences between exotic objects. Instead, they save their energies for the vigorous use of metaphor. Thus, you might be thinking, see this argument - see mince. But can a leader, top person or manager really be someone who (defiantly) calls mandarins "wee oranges" in the upper echelons of society? Can you say "aye" in a Scottish court without being done for contempt (it did happen in 1993)? Can Scots confidently bring their whole selves into the limelight - and particularly into the highly contested domains of arts, and the environment where "proper-sounding" people abound?

If this was easy to measure or remedy, Scots would have cracked inferiorisation, a problem observed across the world where less dominant communities hesitate before asserting or developing their own values. So, of course, it's impossible to say what proportion of top appointees "should" be Scots, impossible to say which individual non-Scots have sufficiently understood the Scottish zeitgeist to become "honorary Scots" and which are stubbornly "rolling out the barrel" in defiance of all local tradition.

The last thing that would be natural for a trading nation like Scotland is an unwelcoming reception for anyone who wants to come, visit, live or leave. The last thing that would ever be appropriate in this "mongrel nation" would be a state-prescribed monoculture of (inevitably) synthetic Scottishness to replace the current and decidedly synthetic model of "Britishness". But the question remains. Is Scottish culture in the hands of Scots? It's a subjective argument - but that doesn't make it any less important. Just much, much more sensitive.

Before devolution, the average Scot stood on the sidelines and watched for decades - maybe centuries - as people with different habits, accents, vocabulary, cultural preferences, reading material, university backgrounds and presumptions about life got almost all Scotland's top jobs. Of course, some of those "leadership voices" were "educated Scots". But educated in what? Scottishness? Indeed, what is that anyway?

It wouldn't matter who was in charge of ­Scottish culture if we were all singing from something like the same hymn sheet. We aren't. When there are two competing realities, but space for only one narrative, it's the official British version that tends to prevail - and since 1707 that has only sometimes coincided with Scottish reality.

As the Englishman Edwin Landseer was painting the classic image of the Scottish Highlands, The Monarch Of The Glen, in 1851, thousands of real Scots were being cleared from real hillsides to make way for deer. This idealised hunter's image of the noble beast became the classic portrait of deer in the Highlands - for some. But for native Gaels, that place would always be occupied by a different man - Duncan Ban MacIntyre, a century earlier, reciting a poem from memory to a pibroch pipe tune which described deer and mountain life in a very different way.

In Praise Of Ben Dorain was transcribed by the son of a neighbouring minister, and much later translated into English by Hugh MacDiarmid and Iain Crichton Smith, who said of it: "Nowhere else in Scottish poetry do we have a poem of such ... grace and exactitude." Despite such praise from the venerated Crichton Smith, educated Scots probably don't recognise the name of Duncan Ban MacIntyre but have seen Landseer's Monarch. Whose reality gets pride of place? The official or the unofficial, the British or the Scottish?

Perhaps, you might think, a cheerful amalgam of all outlooks and artefacts is possible. Why not let a thousand flowers blossom? After all, in the modern world, many cultures co-exist, enriching and enlivening one another. That's true. But choices still have had to be made. For our national galleries there's just too much to fit in. With limited funds and only so many square metres of gallery wall or museum floor, one artefact taking pride of place means several others must go into storage. What goes and what stays? Indeed, is an institution like the Scottish Portrait Gallery meant to capture the zeitgeist of modern Scotland at all? Reaction to the gallery's recent renovation has been overwhelmingly positive but I found myself mightily disappointed by the relative absence of modern Scots on display and slightly bored by "imperial history". Hey ho, I thought. That's just me.

But then six months later, the genial giant and subversive sculptor, George Wylie, died and I found myself mourning his absence from life … and from our National Portrait Gallery. Wylie fused together everyday life, industrial heritage and Glasgow humour like the master welder he was, with installations such as the Straw Locomotive, the 80-foot Paper Boat, the giant nappy pin outside the Glasgow maternity hospital and the Walking Clock outside the bus station.

In a world where "high culture" has long been the preserve of the few, George was a feisty, thrawn, characteristically Scottish and democratising force. Everyone who saw his sculptures could hold an opinion about art. The Straw Locomotive hoisted up on Glasgow's Finnieston crane was fun, daft, spectacular and - swaying gently over the largely shipbuilding-free landscape of the Clyde - profoundly sad. The man was universally popular. And yet, there is no image of George Wylie on display in Scotland's Portrait Gallery. Indeed, as far as I can see, other important artistic contributors to 20th-century Scotland are missing too.

Poets like Norman MacCaig, Sorley MacLean, Iain Crichton Smith and Hamish Henderson. People like the current super-league of artistic talent from Makar Liz Lochhead to Poet Laureate Carol Ann Duffy and Booker prizewinner Jim Kelman. In fact, the list of well-loved, internationally respected modern Scots missing from the walls and plinths of the Portrait Gallery is huge.

Of course, there are reasons for that. The Gallery was banned from commissioning portraits of living Scots until the early 1980s, so the collection is inevitably skewed towards high-quality older pieces. But once again, there's no getting away from the tyranny of choice.

The Gallery owns 3000 paintings and sculptures, 25,000 prints and drawings, and 38,000 historic and modern photographs. So even with extra space, tough choices have to be made. The hopelessly inadequate ground-floor space means sculptures and portraits of modern Scots are kept in storage and shown on rotation. I'm left with the feeling "my" Scotland isn't in there. More importantly, I didn't expect it to be.

Long-term English residents in Scotland are often aghast at the lack of support given to uniquely special bits of Scottish culture. The problem in Scotland is not "Englishness", but the vast amount of cultural space given over to a relatively hollow, uninspiring and redundant Britishness which offends against the Scots belief in the vigorous union that created the welfare state and the Scottish way of doing things, bolstered during recent centuries by our independent institutions and by our resurgent and diverse Scottish cultures.

If the vain attempt to marshall all diversity on these islands into one dominant narrative could finally be abandoned, each nation could plough the lion's share of its cultural cash first, foremost and unapologetically into its own culture(s) and its own understanding of world culture, in which the others may or may not play a part. Who knows, one day - if a heartfelt parity of esteem returns - a genuinely shared British culture may emerge.

In the meantime, though, Scotland must re-order its priorities.