Kojima's original design document is out there, it's a really fun read. I know there was at least one boss that was cut, who the room you fight [MGS2 SPOILER] Vamp in was designed for. Arsenal Gear crashing through Manhattan was also cut because of 9/11, but I don't remember if it was playable or a cutscene.
I just finished MGS2 last week, and it's definitely an amazing game, probably my favourite of what I've played so far (on the third Boss of MGS3). I'd bounced off the controls a good few times, having owned the HD collection for over a year without getting through the Tanker, but it really fell into place after I'd played MGS1. I wish I'd played it at release, the Raiden bait-and-switch is a pretty big part of the overall theme and it's all I'd heard about the game, but I still think my favourite thing about it was how it played off all the expectations I had after playing MGS1. I love how the essay people have probably already linked (http://www.deltaheadtranslation.com/MGS2/DOTM_TOC.htm) talked about the game playing off three "maps": The Series Map, The Scenario Map and the Solid Map.
I'm actually pretty underwhelmed by MGS3 at the point I'm at, the new free camera is pretty cool but I haven't felt it really changing the way I play. The most significant change is the removal of the radar, which I actually really like. I kinda relied on it too much in MGS2, so having to identify these camouflaged enemies feels fresh. The story hasn't gripped me yet though, which surprised me considering people say MGS3 has the best characters. The first two bosses are pretty bland characters that feel like they're just there as progression markers, they appear suddenly and leave just as quick. Snake's relationship with Big Boss is interesting, but apart from the start of the Snake Eater mission they haven't really interacted much. I'm hoping it starts to pick up, but I'm starting to feel like I'm pushing through it just to get ready for The Phantom Pain.