was reading up on what to look forward to in the new expansion, and having a think about what I like about Sins. Mainly, teh lack of mirco managing...
I take it you've never countered LRF with a flak pack before? 
One way to improve combat, without ruining this balance might be to add in the ability to queue up tactical orders before a ship jumps into combat. Like in Gratuitous Space Battles, or Dominions3. Such as "protect captiral ships at all cost" or "take out enemy space station" or "nuke enemy planet and then retreat." Potentially, it would be interesting to experiment with removing player control entirely from battles. (I doubt it would work in but I'd be interested to try it as an option). So that way, scouting and planning ahead would be essential.
Thoughts?
If you're interested in taking out a choice target or two, you could just select the ships you want and then order them to attack the target, and then shift-move retreat back to your planet.
(Holding shift queues orders - you can do exactly what you're wanting with the existing game)
A problem though is that "protect captiral ships at all cost" is a bit vague. When fleets are of a decent size, there isn't much your own fleet can do to protect its own ships, other than to fire at the enemy fleet and hope you kill enough of the enemy's frigates such that they'll lose overall firepower faster. Hold position / Auto-attack will often be the best method, at least if fleets aren't moving.
Your only real way to "protect" your capital ships (other than of course having repair cruisers and Shield Projection and hull/armor/shield research) is to manually retreat them when they get damaged enough.