This thread seems to be attracting a lot of replies from people who aren't familiar with the RV-12is and kit packaging per E-LSA.
What I have heard from most people who have built a -12is is that the avionics first works best. You don't have the guess work on routing things because it's documented, you don't have wiggle room on avionics choices and chasing the hot new thing because it's bundled and documented as well. I suppose there is always an argument for the possibility of updates, but again as I understand things both FF and avionics kits go pretty fast on a 12is. I guess you could assume avionics will update and engine won't and roll the dice on deciding your order is better than what Van's suggests because something might change.
I don't know any of this from my own experience, I'm waiting on my finishing kit and have yet to order either one. I intend to order both at the same time if not within a few months of each other.