For me, Character customisation all depends on the protagonist. I like to keep it generally believable, in terms of what the protagonist's character is, if he's a well-to-do business man, or a street hood, will keep that theme, changing his clothes but keeping the general look.
I always think "what would my character want to to wear?"
I can't imagine that C.J would realistically walk down Grove St with a pink afro and joke glasses, and expect to get to the end of the street without being shot dead by his own homies. San Andreas took the customising to a level where it didn't even look like C.J any more, where as in GTA 4, it didn't matter what you dressed Niko in, he still looked like Niko.
I'm hoping GTA V will find a balance between the two, giving more options than GTA 4, but still keeping it relative to the character.