I had a similar feeling when replaying 3, VC and SA a couple years ago. I thoroughly enjoyed SA and VC, but 3 just had a kinda... depressing atmosphere? I don't know how to best describe it, I guess it's due to the main character never talking and thus having very little personality. Claude basically does whatever he's told by whatever person he's working for at the time, at some point there's a falling out and Claude leaves everyone dead in his wake. When I play VC and SA, I get the feeling of playing in a world that is alive, where the main character makes friends, but in 3 after the story was finished I had a hard time thinking of any characters that were still alive. I still think 3 was impressive from a technological standpoint.
Of course, I might be remembering this wrong since it's been some time, and there's also some nostalgia since I played SA and VC when I was young, but not 3.