I hate when I make a huge base, all set to go fight coalition or ronin, and get dummy or browncoats. aside from my personal preference, how could I change what factions that, say, a skirmish defense will randomly choose? If this is even possible, which I think it is.

Open Constants.lua (found in base.rte) up in your favorite editor (notepad or whatever) and edit this line:

rte.TechList = {"Browncoats", "Coalition", "Dummy", "Imperatus", "Ronin", "Techion"};

to include/exclude which ever factions you want.

That should do it for skirmish and wave defense.