Have you thought about splitting up your "attack" fleet? If the AI's are throwing that much stuff at you, that means that they have undefended planets. Also, I found in one game that I played that I could tie up the enemy fleet at one of my planets long enough to take 2-3 of theirs by sacrificing that planet. IE: I lost one, but the AI lost 3 in the same amount of time. Not sure if this would work, but it's a suggestion.
What I target first depends on what they have. If there are significantly more frigates/cruisers than cap ships I will target those first as they die faster and thereby reduce the overall damage output of the enemy fleet faster. If it is a moderate sized fleet then I will target the cap ships first. Specifically, if I am using carriers I will target any flak ships to clear the way for the fighters/bombers. I've also taken to killing the LRM or race specific long range
I have noticed that when you are making frigates and/or cruisers the shows them in groups of 10 in the empire tree when you have the stack option turned on. You can also shift+click on these stacks of ships to create fleets when you have multiple fleets you want to create in the same gravity well. For example, if you had 30 Cobalts, 20 Garda's, 2 Kol's, and 10 Kodiak's all in the same gravity well, and you wanted to make 2 fleets. Let's say 1 fleet with the 2 Kol's and 20 cobalts and
I too have been playing RTS/TBS since Dune II caught my attention all those years ago and I have to say that I feel Sins will have as big an impact on the RTS genre as Dune II did. I am totally amazed with everything about this game. From the beauty and "wow-ness" of the graphics, to the depth of the gameplay, everything about this game is impressive. I have never played an RTS that had me telling myself "one more turn" like this game does. Excellent job!!
Make sure the bounty on the AI is higher than the bounty on you, then you can deal with the pirates while they are attacking the AI or hit the AI when the pirates do so they have to deal with both forces at once.
I would support this idea also
