I think it's my favorite Bethesda game right now. Early on I thought it was kind of boring, then much later on it was getting pretty janky, but I really liked the faction sidequests other than the lame inconsequential Bioware-esque choices you make at the end of them. I mean the "which terrible thing do you want to roll with" part is cool, but I've mostly just done whichever one seemed to give you the most post-faction stuff to do.
There are some head scratching things of course. Environmental resistance is totally useless; I chose it because it sounded interesting as I'm making my way up the tree to get the god-tier stealth abilities, but in reality I've almost never taken any environmental damage without doing it on purpose and haven't even really looked at the spacesuit/pack/helmet resistances after stuff started showing up (early game) with interesting bonus attributes. I feel like they could have made that aspect more hardcore so that, like in...well, New Vegas mostly, you'd carry a radiation suit around because there were times you needed it. Also, the second special ability the MQ gave me seems basically completely useless outside of having something like the ability to get spaced during ship combat (that would be a cool mod, ship destruction killing your crew and leaving your supplies floating in space and you'd have to boost to another ship and board it without running out of dioxygen).