I know that the developers intent is to keep micro management as close to a minimum as possible.

I think what would help that is the ability to issue blanket standing orders to groups of ships.  I thought of this a few days ago when I was playing a game as TEC.  I had a large fleet with around 40 robotics cruisers, and I had researched demolition bots for them.  My intent was for the robotics cruisers to use demo bots to disable the weapons on my opponents heavy cruisers and then use that breathing room to have my heavy cruisers and LRMs knock out his support cruisers.  It was a reasonable enough plan, the problem is that the robotics cruisers weren't going after the heavy cruisers as much as I needed them to, so I selected them all and started manually issuing orders to use demo bots on enemy HCs using the Empire window.  What would've been nice for this situation would've been if I could've issued a blanket order to my robotics cruisers to the effect of "Use demo bots on enemy heavy cruisers, do not focus fire."

Furthermore, I also think it'd be useful to be able to order ships and strikecraft to avoid certain enemies.  I'd like to be issue a blanket order to my interceptors making enemy interceptors their primary target, but to not follow enemy interceptors to within reach of enemy flak frigates.

Basically, in addition to being able to issue specific orders to ships, I think it would greatly reduce micro management if the player could direct a ship's overall behavior.