I voted for MI2. It was the last (besides Tales) that I played--we had 1 and 3 when I was a kid, and 4 was easier to find. I had to ask my dad to buy 2 on ebay when I was in my teens. It was the one I played with the least help (again besides Tales) because as a kid I was perfectly happy to look up solutions on the internet...lol. I found 2 genuinely spooky. It is darker and nastier than any other installment, and I think playing through it "on my own" added to that feeling of danger. The ending thrilled me not just because it was so surreal but because it so unapologetically refused to explain anything--very David Lynch. To me 1 is comforting, magical, makes me feel safe, whereas 2 is DIScomforting, confrontational, more subversive than the already subversive MI1. But this might just be because I know MI1 backwards and forwards from playing it so much more. (I also played 3 A LOT)
I love all the games and I would not say that 2 is superior to 1, which I think is flawless. I guess I choose 2 as my favorite because...it's MORE! MI1 is perfection...and MI2 is an expansion of that perfection! I don't think the others are perfect but I love them too.