I thought of this just the other day, and played around with something to see if it were feasible at all. I found that I could only have a maximum of ~120 different nodes on my vehicle without having the game crash on load. So even a 4x8 base where you'll only be able to build 1x1s on at a maximum height of 4 bricks will just about reach that limit... which just doesn't give you a good enough degree of freedom to be worth it. (Then again, I've only tested this on my system.) I'm not sure whether this applies to bones / mount points as well but my money is on that it does.
I thought of having like a limited number of different bricks available to you and their position/rotation would be dependent on an animation for every possible orientation. It'd take loads of work to do manually though and there's probably still things that would get in the way if you manage to do that (sequence limit? file size?).
There's another idea I had been rather fond of though, read about it as it was suggested in another topic. Basically a nice GUI where you're given the option to set different components/nodes onto your vehicle, like the player avatar menu. You'd have 100 different components to choose from, which could be rather generous if they were fairly sizeable. It'd have to be designed very specifically if the intention would be to be able to create any type of vehicle. You'd be restricted to a single chassis though so it's not like you'd be able to make something from a go-kart to a bus - unless you have something like a "car" chassis and "truck" chassis, etc. Collisions aren't very faithful to the original vehicle shape anyway (open up the jeep) so it shouldn't be too much of an issue when the main purpose of customizeable vehicles is one of form, rather than function, in my opinion anyway.
I thought it'd be cool to do it LEGO racers style - where you design your vehicle for the purpose of racing it out with other players. Some nifty powerup-style add-on and you've got yourself the ingredients for a potentially awesome gamemode.