The engine definitely doesn't take advantage of a beefy machine in any interesting way. But if you want to run at 60fps sim speed, and have the machine for it (which I don't think exists), the Insane option exists for that. It's called insane for a reason. And yes, AI War doesn't use more than two cores, and on non-host computers only one core.
The movement away from large space battles is one both of necessity and of interest. Granted, there are still tens of thousands of ships in the game at any given time, and often massive battles with hundreds or low thousands of ships on a side. And you can still play with the old ship caps, etc, if you have the CPU for it. But with the mono framework, CPU and memory aren't quite what they were on the .NET side, which was one motivator for the lowered ships default ship caps (though we'd already been moving that direction in SlimDX, anyway).
The move to Unity 3D brings a lot of ease of programming and of use of more advanced visual effects, etc. It also brings general stability improvements on varying computer configurations. The crashes, etc, of the moment are because it's beta, not because it's unity. While I wouldn't deprive anyone of their ability to play the older SlimDX versions (play what you like, of course), those were a real bear for us to maintain for a few reasons, and the technical shortcomings of the .NET installers, our hybrid GDI+ menus, etc, were definitely holding the game back commercially at least to some extent.
The crashes were fixed in 3.716, but we definitely can't fix them if folks don't report them -- so thanks for the files there.
The galaxy map is quite messy at the moment, we haven't gotten to that fully yet.
Probably the resources are not giftable at the moment, that hasn't been reimplemented yet as it was a fairly obscure feature for most people.
The ship colors when zoomed in haven't changed at all, it's either a perception thing or else a difference in screen resolution.