Maybe in the future they'll create a Transformers MMO wherein you can upload a vehicle of your choosing and it will generate a seemingly sensible alt form for it, complete with color customization and even a choice of a range of accents. Choose your own weapons (with restrictions of course, no nuke launchers) and fight using a completely talent-based combat system, not reliant on numbers and algorithms so much as the player's raw skill, kind of like Planetside.
*sigh*
That'd be nice. Oh well, back to dreaming.
the closest thing we have to what you described is the multiplayer character creation thing in fall of cybertron, but that doesn't really let you choose your own vehicle. it's basically just mix-and-matching pre-existing character parts and the altmode is determined by the character the torso comes from (i.e using optimus' torso will give you his altmode, starscream's his altmode, etc). unfortunately, it doesn't provide an actually customizable color scheme (you're limited to 2-color presets). iirc you can choose your own weapons (but they're only weapons that are in the game) and you have a small selection of alternate voices, but it's nothing much.
even then, the multiplayer function is only competitive battles like autobots vs. decepticons, CTF, etc. they're supposedly working on an F2P MMO of the show transformers: prime, but i'm not sure how that's going to turn out.