Miley, the 24-year-old from Inverurie, will be defending the 400m medley at Glasgow 2014 but the English teenager showed that Scottish medal chances will be far tougher in the shorter event.
Miley was the fastest qualifier from the 200m heats but she could not live with the pace set by 18-year-old O'Connor, who had already won the 200m freestyle on Thursday. O'Connor's 2:09.71 was not only a new English record but it was the second fastest time in the world this year.
Aimee Wilmott was second in 2:10.80, while Miley, the champion for six years and then bronze medallist 12 months ago, had to settle for fourth in 2:11.99.
But 24-year-old Miley has had a heavy workload over the past fortnight. She won half-a-dozen titles at last week's Scottish Gas Champion-ships and she had the consolation that her time was her quickest of the year. For O'Connor, it was another outstanding performance and she is not only looking to medal at Glasgow but also at the 2016 Rio Olympics.
"I'm really happy with the swim," said the teenager who trains alongside Scot Michael Jamieson at Bath University. "I went out fast and didn't have a lot left coming down the last 25m. But I really dug deep."
For the University of Stirling's Ross Murdoch, there was yet another superb swim in the 50m breaststroke. He was the fastest in the semi-finals in 27.57sec.
On Saturday, Murdoch won the 100m breaststroke in a Scottish record 59.56sec, Michael Jamieson took bronze and seventh-placed Craig Benson completed a Scottish hat trick by clinching a Commonwealth Games nomination time.
For Jamieson, third place in 1:00.53 confirmed that he will be concentrating on his favourite 200m in Glasgow where he will be aiming to go one better than his Olympic silver medal.
As for Benson, his 1:01:50 swim ended a year of misery. He qualified for the Olympics at the age of 17 but then failed to make Team GB at last year's World Championships. Having missed the Glasgow 2014 breaststroke qualifying at last week's Scottish trials the British Championships was his last chance. He made the 100m time and by squeezing home ahead of Edinburgh University's Calum Tait he also made it the Scottish top three.
"It's been a very tough few months and I was so desperate to make the Games," said the 19-year-old. "I knew what I had to do. It is a huge relief."