The ooooonly change in Koishi from faith that I can see is on her basic danmaku, and whether or not she can charge moves (bhuddist). Koishi movecharging is interesting because she gets to charge them ahead of time. I love charged Lightbulb. The AI doesn't seem to really use the other strong melee intelligently enough to ever want them queued, though... her downwards one has interesting movement implications, though.
I don't really see -any- use in long range basic danmaku for Koishi, and as far as I can tell it has zero effect on her specials, so I've been using Bhuddist; the new version of her basic danmaku is so much better this way, I think, it's fabulous. If I'm at close-but-not-melee range and worried about anything I just start spamming it, and it usually works out.
Need to watch Gpop's video a few times and figure out how to actually chain my basic attacks consistently. I keep getting bodied by that darn Nitori loop. I should probably test serious use of Growing Pains too, since I've only been using the other 5 skillcards... I had dropped growing pain in exchange for a spare slot to throw a bhuddism card into.
If her specials change at all from faiths (Or, heck anything apart from Growing Pains changing from direction other then the small rotation difference Gpop noted on the laser) I'd love to know since I could be missing out.