@ElCapitan: Depends on which MGS3 version you play when it comes to better game mechanics. As for characters, I personally don't feel that the characters in greatness differ throughout the Metal Gear franchise. The story to me is also just as great in any of them. Personally, I can't say MGS3 is the best. If someone were to say all of them were equal, then I could agree.
I base my opinion off the finest experience I've had with the games, and while I really enjoyed MGS3 very, very much, it's not as fantastic as MGS, MGS2, or MGS4. I've beaten all of the Metal Gear Solid games multiple times, and it feels like it's been so long since I've played them. I remember getting really good at three, and it got very easy to sneak up on The End and take him out by punching him. That was great times.
So really, I don't want to argue which is the best because I loved them all, but from personal experience, the majority of the time I hear someone say MGS is the best Metal Gear game, it's because it was their first. I know this is about the best PS2 game, and while I'd say it's one of the best games on PS2, it's not the definitive game on that console. Actually, when it comes to three and four, the only thing I didn't like as much in four, was its story.
I like all of the Metal Gear games, and I'd rather not argue which is the better game, because if I were to ever recommend which one to play first, I'd still say to play them in order from the original, to two, to three, then four. After you play all of the original MGS games through, then play the others like Portable Ops (which I can't stand because of the PSP), and etc.