This is a good post. I think every Metal Gear Solid game, whether they are loved or hated, should be applauded for not being afraid to be different.
MGS2 - Different main character
MGS3 - Jungle setting, food & wounds system
MGS4 - Five different locations with breaks in-between
MGS: PO - first to use a mission based format and the ability to recruit, and play as, many different characters (outside of Metal Gear Online)
MGS: PW - base management and a heavy emphasis on extra content (Extra Ops, collectable briefing files), and the first to have a hidden, second ending
MGS: GZ/TPP - open world
That doesn't mean Snake Eater isn't the best.
And I'd argue, in terms of what defines a Metal Gear Solid game, MGS3 does it better than any other game in the series. Any. Easily.
MGS2 is a good game, but it isn't at the level MGS3 is. Especially considering things like level design and narrative.