Having not beaten ME3 yet, I can't truly compare, but I'll be sorely surprised if its ending is worse than Star Ocean 3's. I friggin hate that ending with every fiber of my being.
The whole point of the last 1/3 of the game is too stop Luther from deleting the big MMO everyone lives in or some shit, and after you beat him, HE DELETES IT ANYWAY. And then you get some Care-Bear bullshit about believing you exist or whatever. It's the fact that he does the thing you were trying to stop him from doing that renders the whole fight and last 1/3 of the game pretty much meaningless. And Luther sucked balls at being an antagonist; they don't show him until the end, so you don't even know who he really is, and then when you meet him, his reason for destroying the world boils down to him being crazy.
Actually, I've only beaten one game on this list (MGS2), and I didn't think the ending was that bad. Just waaaaayyyyyy too many unanswered questions.