I guess this is a long shot but, it would be pretty neat if one can control the way the ships behave in tactical combat.

I am thinking about a set of simple rules, attached to each fleet directing them to maybe focus the most wounded ship, or the weakest/smallest/biggest/least defended/etc...

There is a HUGE possibility for improvement of the game in this direction. You can have a tactical management screen with different groups of tactical rules so you can quickly adapt to each battle.

In the technology tree can contain some advanced tactical possibilities.

I really think this can add a completely new layer for combat and it may be worth the extreme coding effort it probably requires.