I don't really understand the targeted market for these boards ... at least for gaming boxes ...with the 6700k w/ 2 cards in SLI being faster than the X99 platform, and now with > 2 cards no longer being officially supported, (you can do it by obtaining a key but you are on your own support wise),. That being said:
http://www.newegg.com
/Product/Productcompare.aspx?Submit=ENE&N=%2D1&IsNodeId=1&Description=asus%20x99A&bop=And&CompareItemList=%2D1%7C13%2D130%2D840%5E13%2D130%2D840%2C13%2D132%2D516%5E13%2D132%2D516&percm=13%2D132%2D516%3A%24%24%24%24%24%24%24
THG will truncate the long link so just click the link and then co[y / paste the above at the end of the newegg url in your bowser.
MSI has 10 SATA ports to Asus 8
MSI has 2 more USB 3 ports / 2 less USB 2 ports
Asus has an extra fan header
MSI Ratings by Board Owners
5 eggs 50% (12)
4 eggs 17% (4)
3 eggs 0% (0)
2 eggs 13% (3)
1 egg 21% (5)
Asus ratings by Board Owners
Asus 40% (28)
Asus 10% (7)
Asus 9% (6)
Asus 9% (6)
Asus 33% (23)
25% more owners rate the MSI at 5 eggs than Asus
70% more owners rate the MSI at 4 eggs than Asus
50% more owners rate the Asus at 1 eggs than MSI
That's pretty consistent with what we have seen since Z87
Prior to Z87 we were almost an exclusively Asus shop ... we took a beating with Z87, had more with Z97 ... now we are pretty much usng mostly Gigabyte and MSI boards.
If spending $230 on either of these boards, I'd look at the
Gigabyte GA-X99-Ultra Gaming which I like better than those too.
Then again, if it was me and the usage is gaming, I'd go for increased performance with the Z170 MSI XPower Titanium which to my eyes, (and newegg board owners), is the best board on the market right now
https://pcpartpicker.com/product/9YH48d/msi-motherboard-z170axpowergamingtitaniumedition