Roxas looks different because of Ventus heart inside Sora, and Namine is Kairi's heart inside Sora, that's why they're so different (Sora is a really bad mom)
Xemnas is totally different, yes, i guess it's because Nomura didn't wanted 3 bosses to be the same, with different clothes.
Now, let's see... Axel had those marks...
Ienzo didn't change.
If i recall properly, Xaldin had some extra bard as a nobody.
We haven't seen Saix somebody (Only in BBS), so perhaps, a scar that was left while he was a nobody would not appear when he became a somebody?(I'm not saying he got the scar as a nobody, i'm guessing)
That's all i remember.
Edit:
This... I've never tought of this, you have an interesting point... I wonder what happened to him.