In LE2 Lua and the other languages aren't equal. There are a couple things you can't do in Lua simply because Josh hasn't exposed the functionality. So for LE2 you are best off using C++.
In LE3D it "sounds" like every language will have the same functionality LE wise. Josh is putting a lot of energy into Lua in LE3D. He wants it to be a big part of the overall engine, meaning if you want to write once and easily have your game ran on all the supported hardware (all PC platforms & mobile devices) it'll be much easier to accomplish if your project is Lua. It's not that you can't with the other languages, it'll just be easier with Lua.
That being said Lua will never be as fast as C++ in run-time, but sometimes speed isn't everything. It's a balance you have to decide on. I will tell you generally Lua is faster to develop with because you bypass the compile step which often leads to faster transition between coding and testing what you just coded. This development time savings can have a big impact once your project gets so large.