MGS2 does have an interesting story, I just wish I didn't have to put up with Rose and Raiden's crappy relationship when neither of them have any chemistry together. I also could have done without the whole "this is what is going on","NO! this is what is really going on" story fatigue at the end. I feel it's largely responsible for why people feel the plot is confusing since it has so many damn red herrings revealed in rapid succession.

On the brightside, I do feel that MGS2's themes have gotten more relevant as time has moved forward, which makes replays quite a treat. It's been received better in the last few years, probably because MGS4 has kind of taken it's place as the black sheep entry, though some may argue MGSV is more deserving of that title.