Main omissions I've noticed: printf isn't quite the same (no 'z' modifier, the 'n' forms are noticeably inferior), no VLAs.Also, standard library isn't POSIX (which is not an omission but a lot of C code assumes POSIX so you'll probably end up having to deal with this).
I'm surprised you mention intrinsics, since VC++ has a wide selection - https://msdn.microsoft.com/en-us/library/hh977022.aspx - and I'd expect, though without proof, the differences between many of those available on both VC++ and gcc/clang to be something you could work around with #define or, failing that, a small inline function (and cross your fingers).
Aside from VLAs, which is annoying, you can work around most of these with wrapper functions and #defines. So I've been pleased enough with the latest VC++. As a long time programmer for multiple platforms, I can put up with a certain amount of deprivation, and having to put in a bit of effort doesn't bother me (all that much). But I've noticed a tendency for people to sometimes assume that "multiple platforms" means "ten different types of gcc+POSIX+fork+pthreads". I'm sure that even shiny new C99-friendly VC++ won't make them happy.