Well, Random and team arenas aren't restricted to either chapter, so you can do those as well as a prophecies-only char would.
Both Factions and Prophecies have a lowbie arena (PvE charas), and Factions is actually bit better when it comes to balth faction, I suppose. There's AvA for Pve/PvP-only players, and Aspenwood/Quarry for PvE players, tho they give 3 faction per kill, I assume RA and TA give more, dunno. I just do Aspenwood/AvA myself.
Sure, there's some skills that are Prophecies only, but I'd assume they can be improvised with some Factions-version of those skills, tho every skill doesn't have an equivalent Factions skill, and vice versa.