Hey long-time lurker here,
I wanted to make a few comments about the mods (although I might get some details wrong, since it's entirely from memory and there's still things I've yet to play with or experience).
I've basically done a full run of BG1 and two full runs of BG2, both with SCS, and the latter with morph's tactics remix, and ascension.
The challenges in this mod compliment the challenges added from these other mods, and it gives a very solid difficulty curve throughout the game which I enjoyed a lot.
I also enjoy fighting 'hordes', especially when it comes to undead, so I'm glad you're not afraid to add lots of powerful enemies to dungeons and boss fights where they make sense. It gives a very different feel from other challenges and fights. I also got great use out of some of the extra spells and some of the extra items are great at giving me more options without feeling like I need to collect the limited set of items in the game to optimise my party around them.
I will also note that from my playthroughs, the Yaga-Shura fight does not seem to be bugged or incompatible with ascension. I recall it was mentioned in the readme that it might be incompatible but I've played it a few times (it's my favourite fight in the game) and no bug has occurred. This COULD be something to do with my mod setup somehow miraculously fixing it, but I don't have any other mods that change this fight.
Unfortunately, I may come across as a pessimist since my only criticism appears much larger than my praise in words. I'll still be installing it on pretty much all my runs from now on though, so don't worry:
With your spell mod, I tried out your undead component (I forgot the name of it) which separated the undead spells. This was really strong in BG1, but the spells didn't scale like the original animate dead spell did. I think this could do with some change, especially if you have challenge encounters, or any other challenge mods. As much as I absolutely love the idea of having different kinds of undead to summon, if the spell doesn't scale with level, then it basically becomes pointless once you hit SoA. This ultimately means for clerics, level 3 spells are gonna have wasted spell slots since animate dead was probably the strongest spell at that level due to it's scaling and the rest are either situational or mediocre. I also felt like the higher level spell version (doom legion?) for the skeleton warriors wasn't even as strong as the original skeleton warriors (although this could be psychological), meaning I'm taking up higher level slots for something that isn't as strong anyway. There's two ways I can think of to improve this component (I know it's still a work in progress and you may have already thought of these, but I'll give my two cents anyway).
First, you could make each individual undead spell scale in some way. This sounds like tedious work and the result might not be very 'elegant', at least to me but I'm not a modder so I wouldn't know.
Second, you could remove having multiple spells altogether and reduce it to a single spell. This spell would be something like spell immunity, where selecting it would give you a menu, except based on your level. The menu would then have a selection of which undead you can summon and would expand over time. Again, I'm unsure how easy this is to do, but I know that atweaks (or PnP tweaks?) uses a menu for demon summoning spells in order to increase the summon variety.
I really enjoy the idea of being a really powerful necromancer who has mastery of all these different types of undead, but because I'm a filthy powergamer I need better incentive to use these spells in SoA :P.
All in all, fun mod with great ideas and I really enjoyed it. There's simply too many components to comment on all of them, but it's very hard to find any that stand out as poor to me.
