Sisters are not a crippled army in 5th edition. Of course there are some costs imbalances and such but they are not unplayable. There are a couple things though that are needed for them and that I would love to see in a new Codex.
New Acts of Faith: I would keep the system even though you are limited by the number of faith points but I think its fun in a way. The one act that could be cool is granting "Blessed Ammo" to the squad. Other than that I think the mechanics are pretty cool. I could also see having an Act that grants Eternal Warrior an IC for a turn just so your Canoness cant get one shotted.
Unit costs: Overall they aren't bad now. Maybe bring the Rhinos in line with the SM and CSM rhinos so make them cost 35. Also maybe bring down the costs of meltas, storm bolters and flamers in line with the SM costs just cause they are pretty pricey. The Repentia's and Penitents could use some cost adjustments as well since right now they are pretty much worthless. Actually those units IMHO need complete rewrites or should be tossed out the airlock.
New HQs: I would love to see new named IC's for the Sisters. Why not have a named Sister that is the master of Seraphim and makes your Seraphims troops or something. Or a Living Saint that allows you to add in Fanatics to your troop list for next to nothing. I could see some awesome possibilities there that could be really cool. There are also some great opportunities that they could do with Inquisitors but they are too many to get into here.
Fast Attackers: Seraphim are pretty cool how they are done today and I don't know if they need many changes. Dominions for sure need some help. Why not make them Outflankers., There are tons of units out there that can outflank and I cant see why they cant not be the Sister's Chosen.
Troops: I really dont see too many problems for Sisters. Of course the Rhino costs need to be adjusted but they are pretty cool right now and have some great abilities. Inquistor Stormtroopers on the other hand seem worthless to me. Why would you get them when you can get a Sister for 1 more point and she has a Bolter and Power Armor. The only reason that I can think of is to use a smaller Stormtrooper squad to throw into an Immolator and then make it a scoring unit.
Elites: Celestines should have the ability to get Blessed Ammo for all their guns. They should be the Sister's Sternguard. It makes total sense and they should also have more than 2 special weapons. They arent a scoring unit and are supposed to be the Uber Sisters. Assassins I wouldnt change much except maybe give them some sorta frag grenade just so that they can charge guys in cover. Repentia's are the unit that really needs help. I don't really know what you could do for these girls except maybe cut down the costs and let them spend faith points. That way they would be a lot more brutal and would have some numbers to absorb all the fire
Heavies: Reducing the costs on Retributors would make them way cooler. Having the MMeltas cost 25 and Hvy Bolters cost 15 just blows. They are not a cost effective unit compared to an Exorcist at all. Immolators are sort of a lame Hvy choice but I have seen some crazy list Spamming with Immolators so I could see how they can be pretty sick. For the Exorcists I think they got it dead on and would hate to see it nerfed. I think they should make the missiles "blessed" to deny cover but all my friends would really hate them even more.
I know its a pipedream these days but I would love to see an Inquistion Codex with all three Ordos combined. It would be pretty awesome to see all the Orders Militant completely modelled out and I think would bring a lot of people to a very underused army.