Well, whenever I hear someone talk about it they always talk about how groundbreaking it was in mixing different genres, how it allowed for multiple ways to resolve missions and how it was a spiritual System Shock sequel. I don't really hear people saying "oh, it was such a great story about this guy called JC who betrays the anti-terrorist group he's working for cause the terrorists are actually the good guys" and such. In most cases it gets praise for its gameplay elements.
Bit of a limited list in my opinion, but nothing really bad there. Also, which Super Mario? lol