Regarding reactor order, I was thinking it would be nice to display a preview of what will happen if you play a module when you hover over it, like where it will be inserted and how the reactor will activate.
The enemy ship getting away every time is intentional, lore-wise you’re “pursuing” the same enemy ship until you finally manage to defeat it. Of course, in reality this is an excuse to save time drawing a bunch of different enemy ships :)
I’m planning to readjust the balance in a post-jam update, so hopefully you’ll find a more interesting challenge then.