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1. Fixing leadership:
My initial thought was that sister squads could no longer tarpit and were subject to sweeping advance. Kyrinov the IC has a rule that makes
friendly units within 6" fearless. Not as good as the book, but he's a decent substitute. He's cheap too, so you can use him as runaround leadership fixer.
New trick: Unit running away falls back into 6" of Kyrinov and become fearless. Also, he's a controllable tarpit. Move him out of range and squads lose fearless.

2. Mid+long range shooting:
The command squad's act of faith makes them releneless, and every model can have a special OR heavy weapon. The squad also has a laud hailer and feel no pain.
The initial thought is take 5, walk around and shoot, but relentless multimeltas in a rhino don't suck either. Also, for those that miss their all special weapon dominions, the command squad can still do that.

3. Hth:
You can buff units in hth by stacking characters. Canoness act of faith gives +1 initiative and preferred enemy. Jacobus gives +1 attack and feel no pain. Celstians are naturally 2 attacks, and their act of faith is +1 strength and fearless. Double canoness in a squad is initiative 5 and reroll to hit. Jacobus + canoness is initiative 4, 3 attacks each, and reroll to hit.
It's not perfect, but it's not bad. It's very similar to act of faith stacking on seraphim in the last witchhunter's book, but without the 3+i saves. Repentia also have fleet of foot now.
THey also start with 2 attacks, and you can buff them to 3 with jacobus. If you must have 3+ saves, the battle conclaves can do it. You actually have a lot of choices. I know crusaders aren't assault terminators, but they cost 1/3 the points. What you can't do (and I would have done it) is double canoness with crusaders. Initiative 5 power weapon stormshield...awww...can't do that.

4. Act of faith reliability:
The simulacrum allows a reroll. With a character in a squad, you usually need a 3+. With a simulacrum, you're rerolling a 3+. If the squad is taking damage, it's a 2+ with a character.
You can make faith reliable in certain circumstances/wargear if that's what you want.

5. Seraphim are the new dominions:
Seraphim pistols rule allow a model to fire 2 pistols in the shooting phase. So 4 flamer templates with reroll to wound, or 4 inferno pistol shots.

Max your HQ slots. Double canoness gives you double command squads, which are the best shooty sister's unit in the book. Stacked canonesses can get you to initiative 5, but you lose out on conclave stuff and kyrinov. Fortunately, canonesses are stubborn. No matter how you mix it, it comes out okay. If you take 1 confessor, you get access to stormshields, and keep 1 command squad. If you take 2 confessor, have 1 be kyrinov and you can do fearless manipulation as well as take 2 crusader squads.
It's not all bad. It's just kinda sad that HQ's and exorcists are the best thing in the book.

Death Cult Assassins are the best CC unit in the book, and cost about the same as the other options, so you'd be foolish not to go with them.