I beat 2 recently as well. I love the absurdity of this series, but 2's end went a little too far with the conspiracies on top of conspiracies on top of conspiracies. It lost some of the personal edge that came with E.E.'s death I thought. I was laughing out loud at some of the nonsense revelations in the last few cutscenes. Which was great in its own way, but still pretty ridiculous.
Now, MGS3 I beat literally less than an hour ago and that's one hell of an ending! It's still completely fucking absurd in some ways, but it's much more grounded than MGS2's ending. It never loses the thread of tragedy woven into the narrative despite the ridiculousness of it all. Off hand, I can't think of a single more effecting video game ending (except maybe Ico or Shadow of the Colossus, but those are incredibly different experiences.)
MGS2 used to be my favourite of the series. I found it really hard to get into 3. But I kept trying, and I'm so glad I did. It's excellent and I agree with you about the ending. Much more grounded and satisfying.
As for effecting video game endings, Red Dead Redemption is at the top of my list.