I played through a couple of years of Skaven. It was interesting, but I ran across some issues.
You mentioned above the issue with being unable to assign nobles until a certain point, but once I was able to assign many after some Skaven inherited titles, the Fangleader was still unable to be assigned even though it appeared on the nobles screen. I had several different castes at this point, including two warlords. I eventually got around it with some Therapist trickery.
Would you consider lowering the room requirements for the Skaven Councilors, if possible? I was hit by two skaven inheriting the position early on, and having two others inherit later was quite an annoyance.
This may be a vanilla issue of some sort, but one of the enclave buildings would not build for the life of me, I believe it was the Pestilens building (it was a few days ago, and that fort is gone now) that would get the classic "Creature occupying site" error after many attempted constructions and deconstructions.
Overall, it was pretty interesting, though I wasn't able to do everything I wanted to before moving on. I'm curious about their weapons, I wasn't able to test them - the different catching tools seemed like they would make an interesting dynamic.
Also, in my excursions to Adventure mode, I noticed (at least) liches and skaven could not open doors.