Scotland's lean opera pickings just got leaner.

Scottish Opera's new season, with just three mainstage productions, offers a pretty dismal outlook for opera fans north of the Border in 2013-14. Welsh National Opera and Opera North each stage around nine full-scale productions per season, while English National Opera's tally runs into the double digits. Even by Scottish Opera's own recent standards (four mainstage productions plus a full-scale co-production with the Royal Conservatoire of Scotland) it's a scant list.

Alex Reedijk, general director of Scottish Opera, is quick to point out that the reason for the reduced schedule is the ongoing work on the Theatre Royal, the £12m foyer extension forcing the venue to close for two months in 2014. The timing clashes with the RCS collaboration, cancelled for the first time in seven years. As for repertoire, none of the three mainstage productions offers the chance to see any new or unusual work.

The doors of the Theatre Royal are due to reopen exactly 365 days from yesterday's launch with a production of Puccini's Madama Butterfly – the opera that Alexander Gibson conducted in 1962 to launch Scottish Opera itself. It's a fitting nod to company history, and an occasion that warrants a fresh production, but instead we get a revival of David McVicar's much-admired version from 2000.

Luckily the first of the two new mainstage productions is sure to be strong, coming from the director-designer team of Sir Thomas Allen and Simon Higlett, who have already done excellent things with The Barber of Seville (2007), The Marriage of Figaro (2010) and The Magic Flute (2012). Now they turn their attention to Mozart's Don Giovanni, whose title role Allen has performed himself more than 300 times. "It's a deeply-seated collaboration," says Reedijk of Allen's work for the company. "Tom reflects my taste, and as a storyteller has found a great ability to connect with our audience.

"He knows what it's like to be on stage and be asked to do something that's physically impossible and doesn't support the narrative. He's obviously a fantastic musician and he loves entertaining people."

Reedijk feels legitimately proud of having offered the veteran baritone some of his first opportunities to direct professionally. Their discussions "coincided with Scottish Opera's need to have a good bunch of legacy productions, and like Besch's Tosca – still going strong 30-odd years on – we plan for these shows to be in our dressing-up box for the next 20 or 25 years."

The season's other full-scale production comes in January 2014. Donizetti's Don Pasquale will be "a bit of winter cheer", says Reedijk, from the French Canadian directorial double-act of Renaud Doucet and André Barbe. They saturated Massenet's Manon in boisterous bling in 2009, and they should do fun, frivolous things with Donizetti's daft comedy.

Off-stage the big talk is of Emmanuel Joel-Hornak, who arrives as music director in August. It took a two-year "discreet headhunt" to whittle down possible candidates for the post. Asked why the French conductor came out trumps, Reedijk shrugs: "He makes me laugh a lot. He's the kind of guy who arrives in a city and figures out where the art gallery is, where you can get good coffee... he really lands in the community."

"He's got a lifetime's experience conducting opera. You can drop him in any pit and he always lands on his conductorial feet. He's unflappable, and a deeply experienced music maker." Reedijk says he has "not quite got to the bottom" of whether Joel-Hornak comes with any particular repertoire specialism, but says that "for a French conductor he's got a lot of experience in German and Italian music. Certainly there's no lack of Gallic enthusiasm".

Outgoing music director Francesco Corti will conduct the run of Don Pasquale, dates already in the diary before Joel-Hornak was appointed. Reedijk remains vague about the musical legacy Corti leaves the company: "He's a good guy," he says. When it comes to summing up the 2012-13 programme – Scottish Opera's 50th anniversary's season – he says: "I've had a great time, and I think the audience has too."

But is that enough when Scottish Opera's identity is fragile from the loss of its full-time orchestra? The anniversary was a chance to celebrate and consolidate its proud history. "The season has articulated all the values of Scottish Opera," he says, listing "the four strands of DNA to our company" – main stage work "as the composer intended it"; small-scale touring; education and outreach; and new work. "We also tackled the three composer anniversaries [Wagner, Verdi and Britten] and stayed true to a balanced-basket approach to programming. I think it's been a s***-hot anniversary."

The main productions of 2013-14 look like crowd-pleasers, but of course there's more to the season than what appears on the Theatre Royal stage. Dominic Hill's 2005 small-scale production of Verdi's Macbeth will be revived at Glasgow's Citizen's Theatre and Edinburgh's King's in March and April. A co-production of American Lulu – Olga Neuwirth's chamber reworking of Berg's opera – opens in Bregenz in early August before a run at the Edinburgh International Festival. Kally Lloyd-Jones's 2010 production of Seven Deadly Sins is revived during the Fringe, and a new work called Dance Derby tours Scotland late this summer. There's the usual Opera Highlights tour and a touring production of Handel's Rodelinda, plus a one-off concert performance of Puccini's Turandot in the Usher Hall.

Reedijk says each season should be considered in the context of its neighbours, working through a three-year rolling cycle so that this year sits well against the previous year and the next. But what that basically translates to is this: a programme that equivalent houses would present within a year is here spread across three or five.

Subscription and priority booking opens on May 28, public ticket sales on June 24; scottishopera.org.uk