I don't think it's possible to do more than the custom weapon customization, sadly. Otherwise I'd have plenty ideas (such as different kinds of ammo for the PMG, a deployable missile launcher system, shield generator or heavy mortar instead of the E-Web for the officer, etc.). As far as I'm aware, not knowing much about coding, the closest thing you can get to customization is pickup kits or a system in which you spawn alternative kits for yourself with the commo-rose or codes sent to the server as chat messages.

What I've been considering, though, is a weak, barely noticeable hue covering the screen when flying rebel starfighters, to simulate the orange visor worn by Rebel pilots. Maybe we could also have a breathing sound effect (YT link) when flying an Imperial fighter (though not as intrusive as the one in the video ). Maybe whoever is tasked with coding such a feature could make the pilot breathe faster, a bit more frantically, when the fighter is badly damaged.

Vanilla has the option for heavy armour, which drastically alters your appearance.
Presumably you could do the same for Rebel Troopers offering them Visor down/up (not neccesarily with any kind of armour benefit) or as Gurd once suggested, a choice between male or female rebel models.

As he's usually medic and therefore the squad chick by default.

''Its over. Angel won.''   RSF Gurd

We've tried to make that work before Angel, and we were unable. The Character menu is a very tricky business, it was difficult enough to add in another class and enable weapon customization.

"Munchkin: One who, on being told that this is a game about politics and intrigue in 17th century Italy, asks to play a ninja."
— Andrew Rilstone