Ive played with a lot of different fleet compositions over the years, but I always keep coming back to outfitting ships with long range beams and using plenty of high end bombers and fighters. Ive also noticed most people think beam weapons are underpowered but they fit both my playstyle and the need to conserve fleets in starsector.
The biggest end game limitations are the number of officers you can have(10) and the maximum supply cost of fleets you can take into battle(usually 250-300) so that's what needs to be kept in mind when building the ideal fleet. My end game fleets are 8-10 Odysseys and 0-2 auroras with trident torpedo bombers and xyphos heavy fighters in a 3:2 bomber/fighter ratio. In a typical late game fleet battle I send out 15 tridents, 10 xyphos, 4-5 odyssey's and 0-1 aurora.
late game aurora load out with ideal officer(In the early/mid game before you get odysseys replace reinforced bulkheads and a few capacitors with augmented engines)
late game odyssey with ideal officer. The fastest, longest range capital in the game with some nice missile throwing and torpedo bomber resupplying abilities.
the good stuff...
Early on though the major problem is lack of funds and access to rare ships can sometimes be a problem as well. With that in mind the mainstay of my early fleets are sunders and gemini freighters with any auroras and high tech fighters and bombers I can scrounge up, along with gladius and warthog fighters as a decent early game substitute.
crushing capitals from 1500 range like it aint no thang. Graviton beams to strip the shields and a High intensity laser to vaporize armor and hull with an atropos torpedo coupe de grace.
versatile,cheap, easy to find, plenty of supply/fuel storage and a flight deck, dual flaks + pilum for support. Whats not to like?
The auroras and sunders are a very synergistic duo, auroras in this configuration dont do too well at taking down enemy cruisers but they melt the frigates and fighters that normally wreck sunders, and sunders do excellent work against the heavy stuff. As fleet battles get larger and more deadly though, the sunders fragility becomes a liability, not because you might lose an easily replaceable sunder, but because losing the sunder endangers the officer you're trying to level up on it, so sunders and gemini get replaced with oddysseys as they become available. Ive faced all sorts of vengeance fleets and 1,000,000 credit bounties and have yet to even lose a single capital ship using this composition. To add to the flavor, all the line ships use high energy focus as their special ability and all your main weapons(High Intensity Laser, Graviton Beam, Tactical Laser) have 1000 base range and 1:1 or better damage:flux ratios. Tri-Tachyon should be your best friends if you want to use this composition since they sell all the ships and weapons needed for it.