whether C# and java can be as fast as compiled to machine is an old debate but I'm on the side that a good optimizing JIT will make up a lot of ground (no self respecting VM will allow itself to remain in interpreted mode for long)
Liked specifically for this part. I've always held that a tool is only as good as the person using it.
As for Microsoft not using Java, I believe that stems from back in the day when J# was a thing, and Sun basically sent them a C&D over it. I also find the discussion on openness quite ironic since it is due to Microsoft's open documentation and standards on the .Net Framework and VM that allows the Mono project to flourish as it has, and Java's own documentation and standards are quite closed. Both sides, I can understand: allowing other people to work with your stuff and find new ways to use it can be cool, but on the other, I also understand not wanting people to screw with your product and redesign it for things for which it wasn't intended to be used.
However, all of this speculation is
assuming that Microsoft will do anything with regards to Minecraft's development. Mojang is still there, minus like, three people. They're still the development team, and its still their project. Honestly, the most I see Microsoft doing with regards to Minecraft's development is keeping it on the rails so Jeb and Co don't get distracted by the newest mod feature they want to add to vanilla with a completely bollixed implementation.