I would suggest the MSI mobo as well over the Asus.
As for the ATI/Nvidia incompatibility issues my 2 cents:
If the mobos were true SINGLE SLOT PCI-E 16x mobos (no X-Fire or SLI) then I believe that there wouldn't be any issues at all as there would be absolutely NO advantage, either real or perceived, gained for either company by having a "proprietary" product.
Now w/ the advent of SLI/Crossfire platforms which are not cross-compatible (by design) then there can exist some incompatibility, especially on any mobos that are not classified as "mainstream or general usage" using either an AMD (ATI) or Nvidia chipset onboard. My EVGA 780i FTW mobo is a prime example of this. This mobo is classified as an "enthusiast" level mobo--not mainstream/general usage. The PCI-E 16x slots on this mobo do not necessarily hold to the expected industry standard--they are set up specifically to optimize Nvidia SLI/Tri SLI usage & as a result some "standard" PCI-E devices will have issues operating or simply will not work in it's 16x slots. Been there, done that.
At this level neither Nvidia/ATI can be held liable for not "ensuring" cross-compatibility as these types of mobos are specific-usage (modified), not general usage.
We must not lose sight that in Intel's chipset this is a 3rd party chipset (not manufactured by either Nvidia/ATI) & as such can (and has) made stipulation that BOTH platform's technologies will be supported on any mobo that their chipset is being used on (starting w/ the X58 & up). This forces BOTH Nvidia/ATI to "play together" & thus ensuring standardization.
My 2 cents. YMMV & you may not agree w/ this synopsis.
If I were to be looking at any mobo these days I would answer this question before I start looking:
"Am I going to want the mobo to support both vid card maker's technologies?"
If the answer is yes then I would be looking at Intel X58/H55/P55 equipped mobos to ensure this.
Done.