Hmm. I've been reading other people's posts but not really contributing at all. Mostly because I'm not all that sure what I'd like to see in an army.
The suggestions thus far are good ideas. Some Ordo Xenos stuff would be great. Radical/Puritan divisions and options would be fantastic. Being still able to run a pure Sisters/Knights army would also be a good move...
I wonder if something like this would work...
Inquisitorial Storm Troopers are a open to everyone troops choice. Maybe an IST heavy weapons team, too?
They could be upgraded with veteran skills depending on your HQ, or maybe just favoured enemy rules? Xenos = any xenos (too much, perhaps?) Witchhunters = psykers, Daemonhunters = Daemons...
Maybe different weapons options as well...
Having Deathwatch as an option could be interesting, too.
But I'm forgetting the Sisters! Really, I don't know what I'd like to see with them. I already like the minis. I already like the fluff. Sure, I know some units could be improved markedly, which could then make for some variety in a witch hunter's army. That would be nice, rather than having to see "If you're playing for fun, take whatever, but if you want to win you must take this..."
Meh. I try not to get too in to thinking what I want for a revamp, because I know GW will have different ideas. And will possibly balls everything up terribly, as seems to be their want at the moment.
Although, with the current 'New-army-must-be-best' syndrome that seems to be around... Who knows? Do we dread the thought that Witch Hunters/Grey Knights might actually become popular?