Something I've always wanted to see in minecraft would be the Creepop, baby creepers with better design than "scale=-50% creeper model" like below (and its adorable!!!).
[img width=500]
I know underwater mobs and dungeons have already been discussed so i won't comment on that. But I've always wanted to see more passive or passive/aggressive mobs in minecraft. Creepop's (as my example) would be adorable and react to being attacked by turning a little frown and blowing up, maybe even with a loud "pop" when it explodes instead of the normal TNT noise. Flighted birds of some kind would be fun to hunt down for feathers (in turn for arrows, which reminds me, gravel doesn't seem to drop flint anymore, bug or feature?) .
Also i know Frizzle said he wanted more depth to mobs than "Dire this" and "Dire that" but i think its acceptable to have such as long as you put a little design into it and make it semi-reasonable that the mob is there, Dire pigs (boars?) are fine as long as you can tell the difference between it and a normal pig (tusks? I'd like that), anybody agree with me on that?.