I don't know if the 2.0 version Aetherco's been promising will ever come out, but if it does, there's two things I'd like to see improved:
1) Skill rolls, especially in regards to mundane (non-Time) combat. Most of the time you don't roll, but when you do, it gets awkward. I'd like to see that changed. If they keep it more-or-less as-is, they at least better have a good explanation of why, and better examples of how it works. Graces, hit locations, bouts, victories, blunders, etc, are cool in theory, but rarely seemed worth it in practice. Unnecessary mechanical complexity is not something I enjoy.
2) Better GM advice on how to introduce the players to the Fraternities. Frats are a huge part of Span 2 play, but really hard to work into Span 1 in any meaningful way. Wrapping your brain around time travel is tough enough on the new player, you don't want to dump the fraternities on them as well. By the time they've got Time Combat understood, they'll be chomping at the bit to get to Span Two (with multi-year jumps), and not focused on learning a whole bunch of new stuff (such as fraternities). Worse yet, it's too detailed to do as an in-character exposition dump, you'd bore the players to tears. You'd like to do it bit by bit, by introducing a character from each fraternity gradually during Span One - but that would take like 10 NPCs.
Other than that, the game's awesome. Love frag. Love the setting. Love being able to travel through time and space at will.