I suggest changing enemy bosses in PvE to destroyers just because.
They could have the same weapons and abilities, but as destroyers it would just be so much better.
Also, add destroyers to enemies in PvAI so that you can’t just wipe them all off of the map in a matter of seconds.
Maybe NEW missions with a number of ships being destroyers instead of changing current ones?
Considering that this would require a significant amount of work on the AI, I’m not sure that it will happen anytime soon. It’s certainly a nice to have, and I’m the last one to complain about an AI improvement. But, you know, limited resources and such…
Also, I consider the new “vs AI” mode damaging for the game, because it drains the already small pool of PvP players even more. I would strongly advise against pumping much more resources into it, unless it gets changed to be limited to newbies (and no, ranks 4-9 are NOT newbie level in the current game design).