Some X99 (ASUS) now seem to include a 2 port USB 3.1 PCIe card, I think this is just recent, Z97, 2 onboard, @ 10 G/sec, I guess their battling it out and trying edge out TB it seems, I'm not sure if USB do the 4K video stuff yet. I guess its hard for audio interface industry to keep changing designs with PC world, where nothing is static/stable week to week, at least USB is backward compatible so far, Firewire may still adapt with TB I believe. I saw the RME MADI interface with USB 3.0, 394 I/O @ 192k, oddly now cant seem to now access info on RME site. Does the gaming world, (mostly driving high end PC market) really need USB 3.1, to connect game controllers, and/or mouse and keyboards, (or even recording interfaces). I'm not sure who 3.1 caters to even right now, they surely don't need TB to do this anyways, and apparently not too concerned about shares of some recording industry trends. Maybe recording interfaces should all be including an ETHERNET I/O to be more consistent, I think I read the MOTU may allow ETHERNET port to act as the DAW interface also?
In my case at this time, if USB 2.0 can cleanly do even 16 I/O simultaneously, I would be more than OK, in my home studio, (while also using other USB ports for MIDI devices, and other peripherals). If I had the TB option on PC and interface though, I would for sure use the TB interface.
AS a note since I recently installed an SSD as main drive for OS and Sonar to run on I rarely now have any audio issues I had using HDD, like clicks, drop outs or crashes etc.. as you've mentioned, recording or processing/mixing many tracks and FX. (@ 96Khz).
 
Cheers

4K video would be a reason to get the x99 for sure. I know for what limited video I do (cyberlink powerdirector) it was a big jump in reducing rendering time when I switched to the 4770K.  My feeling is firewire is at the mercy of Apple, it will die when they kill it. USB  3.1 is going to be worth it just because you will now have a less than 95% chance of plugging it in backwards. MOTU already allows the ethernet port to act as the audio interface, on a Mac that is.  We currently have 24 channels i/o, so that's a good start and many more are coming soon as MOTU has stated it is priority #1 on the windows side. A small SSD drive might be a good idea for tracking, no need to use it for storage, so you could get away without having to spend too much, good idea.