Clothing, Mesh customisation, Optimal set-up?

As far as I understand, you can't really have heavy character customisation (muscle tone adjustment, scaling etc.) and at the same time have unique clothing which isn't just a change of texture. Is this true? What are the practical limits to making a RPG, with regards to a character's mesh that can change over time (think muscle growth), whilst being able to change clothes at whichever stage the player wants?

Would it be optimal to leave out one or the other? I was thinking of the muscle tone changes in San Andreas, when you pump weights. I imagine that the texture stretch would be no real problem there, so if anything, that kind of approach might be best. Subtle changes over time that don't really affect clothing at all. But if the clothing involves separate meshes, for instance, changing from trousers to a tunic, you'd probably need to have separate animations for every muscle tone wouldn't you..

Animation 1 = small muscles + clothing mesh type (tunic)
Animation 2 = medium muscles + clothing mesh type (tunic)
Animation 3 = big muscles + clothing mesh type (tunic)

Animation 4 = small muscles + clothing mesh type (trousers)
Animation 5 = medium muscles + clothing mesh type (trousers)
Animation 6 = big muscles + clothing mesh type (trousers)

etc.. Which is obviously a lot more work and doesn't offer the gamer much more really.

So.. I'm thinking the optimal set-up for character mesh + clothes would be:

1. Character customisation at start involves changing skin tone and facial features only.
2. Allowing muscle growth, but subtle. The best muscle tone you could hope for would be noticeable, but wouldn't stretch textures too much. Only allow muscle growth around parts of the body where clothing mesh differences do not exist. Like shoulders, arms.
3. Have separate meshes for the different types of clothing, with texturing and alpha defining the different shapes. These meshes would each have their own animations I guess, or change bone weights, at least. (Could you technically have a mesh that would be a collection of all the different clothing type meshes, and then for each clothing piece just alpha out the types you don't want to use, while texturing the UV's for the mesh type you want to use?)

How do you change a character mesh slowly over time anyway?

Any info on my general musings would be great