I've got a lot to say about MGS2 that I know many here will disagree with, but hear me out.
As far as being a game is concerned, I did not like the inclusion of tranquilizer weapons. It feels like a cheap way out of making it possible for there to be a no kill run, and it effectively makes stealth braindead to accomplish (unless you're playing on the highest difficulties, something most people did NOT give the game enough of a chance to get up to trying). The second act of the game is pretty much one of the least fun things in MGS that isn't playing through Act 3 of MGS4.
The Big Shell is more complex than the tanker and is a larger area to explore, but in terms of design it was not as interesting to me visually, or even from a gameplay standpoint. I'd have preferred that more time was spent on the tanker, and while it was important that the Marines get removed and replaced with Russians immediately, I'd have liked your time on the tanker to involve stealthing around the Marines BEFORE the Russians came onto the scene.
The boss battles I felt were mostly uninteresting to me. As characters, Dead Cell did not have quite the same appeal to me as the bosses from MGS1 and later in MGS3. The RAY battle at the end was tedious and felt like it dragged on for too long even on the Normal difficulty. Limiting the actual final boss to the use of the sword (that I did not care much for the controls of) did not make me enjoy the fight despite the actual idea (sword duel, but the other guy is more or less cheating) sounding badass by itself.
The Harrier, however, was the best Boss fight of the game (and among the best of the whole franchise IMO). After more or less getting cockblocked out of a proper fight with Fortune, and the disappointment of Fluffy Rollerblade Guy, the Harrier is an intense battle on a bridge RIGGED TO EXPLODE (and it DOES during the course of the battle). Compared to what it was supposed to be an analog for, the Harrier is way more exciting to fight. It can do comparatively more and its capabilities were used in interesting ways.
As far as the writing is concerned, I would have been happier by omitting Rose in her entirety. Whatever message she was a part of to the player, I did not give a flying shit about what day it was, nor did I care for any of the conversations she held with Raiden. It was an extremely ham-handed way of trying to inject drama into an already pretty dramatic situation. I'd say this is a problem with most of the Big Shell chapter (and MGS 2 as a whole): all of the writing and the drama just happens to conveniently have gathered all of the players together. Even before the final scenes played out, I was just not able to care for Otacon's drama. Emma's tragedy was preceded by an ESCORT MISSION (and I profess to hating these in almost every game I've ever played so it really colored my judgement of her character arc), and I never felt compelled to care about her, or care about protecting her.
Raiden himself I actually don't have an issue with as an idea, and I appreciated the idea that he was to allow us to see Snake from the "outside" as it were. It was the execution that bothered me. I've read multiple analysis that read him as a character that represents the player, and while I respect that, I don't find that aspect alone making him praiseworthy. It's not that he's whiny, it's that he's whiny in a way that doesn't garner any sympathy whatsoever. I can't believe his whininess. Rather than making his whining feel like the result of actual stress from the mission, it felt written as though "Okay, right now he needs to whine about something because its going to be a change in the gameplay." Ironically, I think Metal Gear Revengeance of all things does a better job at illustrating the character's inner turmoil regarding what he does and why he does it.
I disliked how in MGS1 some of the most important plot reveals happened on the Codec, and MGS2 takes that even further, with that final lengthy conversation near the end of the game. MGS is known for massive exposition dumps, I accept these as part of the series, but heads talking at eachother and pantomiming surprise or anger is the least interesting way of delivering plot I can think of. We may as well have stripped away the in game visuals and replaced them with an FMV of the actors in a booth reading the lines at eachother. MGS3 I think does a better job at juggling the Codec and regular cutscenes of any game in the main series.
However, despite all my own personal criticisms, I'm very happy that we got MGS2 as is. Even before Spec Ops tried desperately to railroad players into doing terrible things and then make them feel bad for it, MGS2 was getting people to actually think about the stories of the games they played. It made them consider alternatives to just blowing everyone away. It got people talking. While it did not necessarily have its intended effect on its entire audience, the game deserves no small amount of praise for having the balls to be what it was, when it was. The only other Metal Gears I've spent more time playing and thinking about are MGS3 and Peace Walker. As far as the "classic" gameplay of the series, it's the best send off it could have recieved before evolving to something greater.