I have a somewhat similar setup - although with a different RME interface - I’ll offer my 2 cents:
Win 7 x 64
Cubase 5 (unfortunately still running 32-bit thanks to Waves plugins…)
RME fireface 800
It depends on what your most common working situations are, but for me the 01v96 is an amazingly powerful mixer and controller, and the I/O and routing are indispensable. The RMEff800 is a little more $$ than the mr816, but it’s vastly more capable - It has 10x8 analog I/O + 16x16 adat + Midi & SPDIF - I got the my16at slot card for the 01v96, and that allows me to route 24 adat I/O ch. & the 16+ analog on the mixer simultaneously with 28x28 ch of I/O to Cubase via one firewire connection…For my money you just about can’t touch that level of functionality without going to a full MADI setup, and it has run smooth as silk for me all the way back to SX3 & Win XP.
The Cubase DAW remote functions are controlled via midi link to the 01v, so I would be willing to suspect your MOTU midi gear is clashing with the 01v’s midi link at the root of any instability…MOTU’s drivers are notoriously bug-prone and erratic, and they never seem to work well with anything else. I had a MOTU 896 as my primary interface back before I got the RME, and I had endless weird issues with everything in my rig until I removed their terrible ASIO drivers. To me the 01v and RME’s stuff are pro-level gear in terms of construction and support - rock solid in my experience and both play really nice with Steinberg software platforms.
Hope that gives you some info…cheers.