Priorities

I'm still a bit on the newb side of things, but heres how I run things.

My first priority are the siege ships.  Normaly, I'll detatch my LFs and send them after the siege frigs on their own. If that's not enough, the fighters lend a hand.  But if I can't save the planet, or don't care about it, I'll just ignore the SFs.

As for chosing particular targets, I go mostly by ship types.  The HC's I  mostly leave to the AI to control.  The LF's do a loop around the area and target support ships, starting with repair ships, then the Carriers, then whatevers left over (run 'em back to my repair ships when they get too damaged). The LRF's are what I run through the queued focus fire bit.  Personaly, I start them off on the LF's to protect my support ships, then que through the HC's and other LRF's.  Of course I break their que a lot, mostly to pick off the more damaged ships.

And the starbase? If i can ignore it, I will, and just come back for it later. If not, I generaly leave it to the Anti-structure cruisers and just use my fleet to defend them.

And bombers... They always start out on the jump inhibitors. Then the repair bays... then the weaker bits of the fleet.

Meh, thats my meager advice.  This is how I do it against the AI.  Probably won't fare to well on-line.

This totally depends on what kinds of units and capital ships both sides have.   There is no catch-all response for every situation.

When attacking an enemy planet, a good top priority is to kill construction frigates so he can't build more structures.  Four or five squads of fighters will achieve this very easily.  After that, repair bays are definitely a high priority.

Deciding whether to attack an enemy capital ship or his units is a tough call, and really depends on whether you can successfully bring down the capital ship or not.  If you think you can, then go for it.  If you cannot, then this is probably a wasted effort and you should attack other units.  Long range frigates are probably the top priority to kill because they are some of the most dangerous.

Yea, i don't know how s/he did it, but last game i was rushed with about +/-30 long range frigates and a level 4 capital ship that specializes in destroying planets (all TEC) within about 10 minutes of the game.  I got so aggrivated.  I think they might have been fed by team mates (3v3).  None the less, i quit, having only 2 planets and he ignored the lesser of the two, which had all my fleets (which still was no match for his), 3 repair bases, and one star base.  My team mates couldnt feed because they had nothing of their own D:

To kill massed long range frigates, you actually should be using scouts.  Scouts are cheap, easily spammable and deal double damage to long range frigates (as well as siege frigates, colony frigates, and other scouts).  Scout your enemy to know what he's building, then pick the right counter-units.  Against this sort of army, your best bet is usually to build scouts or fighters and focus on the LRF.

The Marza dreadnaught is a dangerous capital ship, but a good counter-pick is the Sova carrier.  Fighters are really effective at killing long range frigates, while bombers are good at killing capital ships.  There's very little he'll be able to do about a Sova with a Marza.

If you're Vasari, start the sttack with a shot from your Kostura

If I've got splash damage like TEC EMP, the frigates are easy pickins.  If I've got something like Vasari nanomatter or TEC designate target, goodbye cap ships.