I really think we need to start with the stat-deflate, Super weapon rebalance and Armor rework, turret rework and such before anything else should get started. Those are all deep in the core stuff and will take the longest to make sure that they are correct. Well just dividing all numbers by 100 should be quick. Rebalance of Super weapons and Armor are major things that I don't see being done in less then a month worth of patches without a lot of luck.
Once we know we got those system solid, I think the next thing would be hacking rework. The feeling I get, is that well it is going to be core. It not literally going to be going into the heart of every unit in the game and changing them. I fully expect one patch is going to have something like MKIV fighters missed on the deflate and you get MKIV fighters that are as strong as hunter killers for a while.
After that, a lot of the things can more or less be stuck on to the existing base without blowing up the whole base game. A bad fallen spire event might make fallen spire unplayable until the next patch. A bad rebalance of fighters could make the whole game unplayable until the next patch.
