I'd take the sisters codex
I'd find a good fluff reason why these wimpy T3 nuns can use power armour that needs super strong, genetically enhanced T4 men most of the time.
I'd keep the craziness of the book, maybe even adding more. How about a moving cathedral? something fast that is as crazy as the penitant engine or arco-flagellants?

I'd boost the priests, and the canoness'. How about the ability to "evangelise" your opponent's army? A bit like the old "chapter approved" Enslaver rules - take control of your opponents army, or at least confuse and puzzle them.

Cheaper Sisters.
Remove Allies FULL STOP
Keep faith powers, but make them easier to play (maybe get rid of the martyr thing)
More special characters
More flamers, cheaper flamers