Lots of questions! I'll do my best to answer:
I will definitely not be using the Lemma engine for future projects. It's not a very capable engine; it really only works well with voxels. It's very specifically designed for Lemma. And that's fine, but I'm not going to re-use it for future projects.
I decided on C++ because I'm a control freak. I need to be able to see all the code I'm running on top of. I've spent so much time battling Unity problems, and it's just not fun dealing with other people's code. Unity is fantastic for small projects, but I think large projects end up spending about the same time writing custom systems, upgrading to new versions, dealing with broken plugins, etc. It's much more fun to write your own code than to re-import a plugin for the umpteenth time because it's still not working.
Furthermore, most plugins (examples from Lemma: Wwise, Oculus Rift, Steamworks) have a native component with a .NET wrapper which for some reason is usually out of date or just lower quality than the original product. Wwise is fantastic, but I have never once seen the Wwise Unity wrappers work correctly on the first try. Of course I'm still using libraries for MK-ZEBRA, but it's not too bad because I'm building all dependencies from source (one exception will be Wwise, because it's just so darn good).
Lastly, I've recently been following Jonathan Blow and Casey Muratori and their respective projects (Jai and Handmade Hero) and came to realize that memory management is generally the biggest performance bottleneck in games, and C# makes it very difficult to control memory. For Lemma, I had to write a bunch of custom allocation code to work around internal, opaque implementation details
of the .NET CLR. I spent days tracking down memory leaks and null reference exceptions. The whole reason managed languages exist is to avoid manual memory management, memory leaks, and unsafe memory accesses, yet I had to deal with all three of those while sacrificing the ability to easily arrange memory for optimal performance.
In general, I'm finding it's better to write your own stuff. For example, for Lemma I spent weeks battling the XNA content pipeline to make it properly import FBX animations. For MK-ZEBRA I spent less than a week writing an animation importer based on Assimp, and it was way more fun. (More on that in a future devlog update!)