Yeah, as with any heavily modded games it can take awhile to figure out which ones you want to use and then figure out how to make them all work together.

Hardest part for me is the body/facial animation mods, coupled with the alien races that have their own body types.. or clothing/armor mods that don't always fit a modded body shape.

The new DLC also recently stirred the pot a bit, leaving lots of mods in need of an update. Many are working again, but last I played some were still unavailable.