The reason for Ul'dah being the setting with the scions and yourself being the scapegoats would be explained if all of this is a revenge plot from a villain who was most hurt by this group of people in the past.
The fact that Thancred's time as an ascian is brought out along with Minfilia's echo as proof of our collective guilt, the question has to be asked how any of this would be known? The only people who knew both of those things died during operation Archon when foiling Gaius van Baelsar's bid for power during the time when it was in doubt who would wear the imperial crown. While it's possible a spy was able to inform on the echo from inside one of the city states, the only people who knew Lahabrea was Thancred were only scions and the imperials present.
Gaius van Baelsar was trying to conquer Eorzea for himself as his bid for why he should be crowned when the emperor died. It's stated in the story that cause of these actions none of the generals could return home if they failed, cause this operation was without the blessing of the imperial government. Which is why Nero is wandering around dressed as a vagabond alchemist instead of going back to Garlemald. Our actions were not so much a defeat of the Empire, but us stomping on the dreams of a general who saw himself as a future leader of his nation, if not a nation of his own. However we would have noticed if Darth Black Wolf was in in the back sneaking cheese cubes and glasses of wine. I think the thing to notice is the motion Ilberd uses right before he throws that energy wave from his sword, it's the idle animation Gaius van Baelsar takes when you fight him. The attack itself is just a single slash version of his X slash he uses after teleporting.
If any of that is in the ballpark then the real question is not why, but what the endgame goal of all this is. Is it the continuation of a bid for personal power, or is it a bid to return to the empire a "war hero" when he hands ul'dah over on a platter?