My short list:
1.) Making the VVT control coherent would be peachy.
2.) Fuel control (duh)
3.) Fan control
4.) Control over launch control and NLTS. Specifically, I'd love it if I could control timing retard on at least NLTS. 3 foot fireballs and 20psi full-boost shifts are something I'm missing coming to this car as people put bigger snails on these, they'll want it too.
5.) Most likely never happen, but if we could gain any control over the BCM I'd do a back flip (no joke). I'd LOVE to disable the auto lights, auto locks and other things that make me want to burn this vehicle on a daily basis.