Yeah, I cut a lot of the user-friendliness to get it out in time for MOTY. Expect the descriptions and whatnot to be filled in in v1.1. Also, I'm planning on updating the website with more information than it currently has, so that will turn into the manual in effect. Space tugs, and all utility craft, specialize in repair, by the way.
We think the exceptions are somehow related to bombing runs, but other than that, the exact one hasn't been pinpointed yet. You can bypass them by auto-resolving land battles though, which is the reason they weren't found in testing.
As for the load times, someone on the forums caught that I was using bad LUA syntax by making string literals span multiple lines and now that I've fixed that, it appears
that the mod loading times have improved. But it's perhaps too early to say for certain.
I'm glad you like the new hero system! I'm pretty happy with how it turned out, with the exception of the perma-death bug and also apparently you can build Pellaeon and a couple others multiple times. But it gives me the foundation to add infinite amounts of minor characters to the mod now