First Idea: Destroyable terrain. C'mon, we're in the age of big explosions and fire now, I think it would be a nice touch to see the scarred Earth of where battle had come.
2nd Idea: Auto-Naval Battle Priority. Ever come apon a very juicy and undefended trade fleet that you wish to add to your own, but don't want to have to go through the tiresome work of doing so yourself? Then how about you can have "priorities" set to your auto-naval battle. "Capture Priority", where the AI will put capturing ships at the top of the priority. "No Priority", where the AI will judge things as it sees fit. "Sink Priority", where the AI will not bother with capturing ships, and will attempt for full-out damage and no prisoners shall be given quarter.
Just a few ideas that came to mind quite suddenly and I wished to add them down before I forgot them.