So lets see nearly two years since MGS4 came out.
Some random thoughts since then:
1. I still love the game, it (along with the Database, which is an amazing release and for free) actually took the time to resolve everything. Yeah, there is some retconing, but it never bothered me that much. Resident Evil 5 also did this and never gets enough credit for doing it (considering that series had some mindbending wonky shit to tie up)
2. I wish I could just install the game at once, I understand why they didn't do it, but I just wish later on they created a patch that allowed it as an option.
3. I just never did and still don't like the Sniper battle (the setup and look is great); I'm just not nuts about dealing with all the Outer Haven chicks. I realize other battles have additional enemies at the same time, but this one was just a bit more of a pain in the ass for me.
4. Sometimes I wonder if all the extra weapons and ease to get them, made the game a bit too easy (not counting Outer Haven).
5. Was the story goofy at times, a little, but nothing has and every will beat being told that Otacon did his stepmom in in MGS 2, in terms of weirdness and just creeping me out.
6. Still I love this game, every gameplay moment was bigger than the last and the end fight is still the one of the best of any game I've ever played. Some maybe more fun, but as an overall package and what it represented to the series, it's still one of the better gameplay moments I've ever had....
The best one is still crawling through the microwave room while all those other actions are going on. It's one of the few times I got emotionally involved in a story and started shouting, "Come On Snake, Come On, You Can Do it!" Not because I wanted to beat the game, but because I cared.
Only regret was some asshat on gamefaqs spoiling the major points two weeks ahead of time because he got the strat guide.