While I find that meteor was fun to work with, we ultimately opted for plain-old express + backbone. I think it's abstraction is more of a disservice. It adds a lot of magic and unknowns to the picture.
After a few months, the initial value of having the unified codebase is exhausted, and you're left with the technical debt of having already adopted their libraries and conventions.
It's not really accurate to say that meteor allows you to use any library, you are adopting their conventions. In the end - using a single unified codebase in JS involves going against the grain in many aspects (I can elaborate if you like)