The part that kills 2 for me during replays are the Bomb fetch quest, Fatman boss (I like the character, not the fight), and the Metal Gear Ray(s) fight Well, the more I think about it, the more I remember not liking certain section's gimmicks, alot of MGS2's feels monotonous, But don't get me wrong I love the whole series. 3 truly is the most replayable next to 1. V and 4 have great gameplay. and PW feels like VR missions for MGS3. Also play Ghost Babel
TLDR 3=1>2>GB>V>4>MG>PW>S'sR off the top of my head haven't played PO or MG2 yet