MDIL is designed to solve a different problem than LLVM IR. LLVM IR is an exchange format between a compiler frontend and backend. MDIL is designed to solve certain fragility problems in binaries.

.NET Native uses MDIL to create a looser coupling between NUTC and the runtime. This means NUTC doesn't have to understand the precise binary layout of the runtime. The binder takes care of fixing that up!

MDIL has more advanced capabilities too. For more background on MDIL, I highly recommend watching the video I linked to in the blog post: http://channel9.msdn.com/Shows/Going+Deep/Mani-Ramaswamy-and...