The GCN ports are for full backwords compatibility. DK wouldn't be cool without bongo's, FF:CC & LOZ:4 Swords would lose itself without connectivity, DDR Mario wouldn't be right without the dancepad, MP6 loses it's function without the mic...yadda yadda yadda. Plus, if there's any peripherals or specialty controllers that would require themselves to be hard-wired then those ports could be used for that. The ports could also double as a special recharging station for your controllers maybe.
I'm hoping that the Revolution controller can be used to play GCN games, but whenever Nintendo refers to the "interface" they always say that it'll work well for backwords compatibility with NES, SNES & N64 games...leaving out the GCN games. Cutting out functionality by making it incompatible with GCN games would likely mean that ports from other systems (who use similar to GCN type controllers) would not be wise.
Adding controller slots (like with N64, DC & X-BOX) back would be nice for expansion, but I'm hoping that whatever revolutionary features are BUILT-IN to each controller from the get-go. Besides, there was an oppurtunity to do lot's of things with controller slots in the past, adding slots now just goes right back to those problems of having to buy all these new "paks" to get full function with some games. I'm more liking the idea of having a EXT port that can be attached to different options outside of the controller like the GameBoy mini.