I've spent somewhere north of three thousand hours turning SOA2's abilities into insane workarounds for AI shortcomings, creating random encounters, self replicating objects, variable abilities, etc. The ability system is the scripting engine, and you can do great things with it. Everything else is basically asset replacement.
Sins is a locked down system. You can change everything about appearance, stats, what abilities they have. You can get crazy and do insane things with abilities like some of us nut jobs have. You can not change how things work. You can't make ships have six ability slots instead of five, or make the gui's display things they aren't already designed to read.
The various window files have an ordered list that the program reads from. The event window for instance has the font, duration, and positioning, in that order. The program won't read anything else. We have no code injection system, and the mechanisms by which the window files are read are hard coded, ignore this and try to make it do something else and you will simply generate errors.
Now, if you want to turn the game into a battle between space unicorns with magic for abilities, complete with miscasting, random impacts, species specific restrictions, etc, you can. It would probably take you a thousand hours to understand the ability system well enough to get it all done without referring to other works, but the capability is there.