Don't worry about it, man. I figured those were the reasons. They are all fair complaints, so you'll probably be good with this one. Supposedly it still has some of the "stupid stuff" (not my words) from the previous games, but easily ignorable for an amazing open world stealth experience with great cinematograpy and voice acting.
The controls are awkward and there are a lot of baffling stuff in the stories, so I can't disagree with you, but the pros out-weigh them enough to make it my favorite franchise. I love the social/political commentary, characters, and blend of the stealth/action/adventure genres, and I haven't found a franchise that's hooked me so much as this one. I can be "subjectively-objective" and say that there are better games out there, but those elements are why I love it so much. I think MGS3 deserves to be in a very high spot in the greatest games of all time, but it's okay if you don't like it. There's a lot of people that don't like this series and like that game, so you might enjoy it if you give it another go. There's still some cheesiness, but once you get past the Pain, I think you'll enjoy it.