I like the ASUS X99 Delxue, that's the one I got. It works well and has nice low latency.
USB 3.1 is a non-issue at this point. Nothing uses it, and as a practical matter USB 3 is only used for audio interfaces with a ton of channels like RME's MADI stuff. USB 2 is all that's needed for normal audio interfaces.
Thunderbolt is not needed unless you want to use a thunderbolt interface. The problem with that is that many of them only have Mac drivers so even if you had a TB port, you couldn't use it on your system.
M.2 can be useful if you want to get a really fast M.2 SSD. That is more of a "because I can" thing than really useful though. I have one, a Samsung XP941, and it really offers no noticeable real world benefit over the 840 Pro it replaced despite having much higher benchmarks. Also M.2 is just a small PCIe 4x connector, so you can always add it via a cheap addon card.