I wouldn't say all other foundations for higher-order languages -- F# runs fantastically on the CLR (or Mono) and doesn't have any of those problems you listed.
JVM and CLR are not very different. What would be the reasons to want to avoid JVM, but still consider CLR as an acceptable choice?
Most things work, but there are a few things that are broken in unavoidable ways. Similarly, the performance isn't terrible, but the optimization is not quite at the same place as the original platform.
Xamarin's rapid work suggests that there will be a 'production-ready' CLR for most platforms (they've got it down for iOS, Android, and recently OSX) soon enough.
Right now, they are stuck in the odd middle, but it is still an amazing value if you are building common code cross platform apps.
The Windows-based implementation of the CLR is proprietary, but as other posters have mentioned, it's built around an open, standardized specification (ECMA-335). Xamarin has been making big strides in improving Mono over the past year, and it'll only continue to get better.