Not sure if Jeff (or anyone from SWS) will ever read this, but:
1. The flexibility of the creation system and all the various upgrades you can add is awesome. I am enjoying playing with it to find powerful combos.
2. I miss the ability to use keyboard shortcuts for _everything_, including interacting with objects/containers and attacking enemies. (I know this is not a change that is specific to Mutagen, but it seems like a newer trend for Jeff's game to not have this)
3. The overworld map is... not my favorite. I really miss the way the 2nd Avernum trilogy did it with a full seamless map and no overworld transition. If that's too much to ask, the Avernum 1 remake's style of having a tile-based overworld map is not as good but is acceptable. I'm not a fan of Mutagen's system.
Overall, this is still my favorite SWS game since Avernum 6. I think the story is much more compelling than Queen's Wish, and there's still plenty of depth to exploring (I hated the way QW did away with junk items, so I'm glad to see that come back here).