I think there is already far too much customization available. What military (which is what Star Fleet has become) makes up custom vehicles for every officer? Even if they whine a lot or pout. "You want a pink and green tank with tail fins, go find another line of work."
Smaller (low-rank) ships simply don't have the space or power capacity to be ungraded. Where would you put the extra consoles (and suipporting electronics)? There is only a limited number of cubic meters. You may wish to put a really large engine in your small car, but get a grip: You can't.
Star Trek isn't fantasy. It has a basis in projected scientific reality (with excessive techo-babble added in).
I must admit to having the same problem with the non-uniformity of uniforms.