Cool project! Can't wait to see a pure .NET client with OpenGL down the road. I don't install Java on anything anymore (mostly due to all the security issues) so I haven't played Minecraft in years.
Java was originally marketed as a secure VM sandbox allowing for untrusted mobile code execution: centrally web "applets", but also zero-install desktop apps. Basically, it was attempting to do what Javascript (especially with ASM.js coupled to a browser's desktop-app integrations) eventually succeeded at doing.
When held to those standards, Java has been kind of disappointing—repeatedly oscillating between "just about good enough" and "major hole preventing this setup from working." Likewise, many things Javascript got right immediately (like the FS API providing per-origin virtual filesystem containers rather than a view of the actual OS) were never even considered. Despite the marketing, safe execution of untrusted code was never much of a real goal for the platform, and disappeared entirely as a "tentpole" after 1997 or so (despite everyone still remembering the marketing and thinking Java "should" be capable of that.)
When taken as just another bytecode-VM-based runtime platform like the .NET or Erlang runtimes, used for executing code already granted the same level of trust as the other native code on the system, Java is great.
