I generally follow a fleet doctrine that mimics that of the US navy; that is, based around a carrier vessel, and the aircraft do most of the heavy lifting. My current composition is as follows:
(Note: I run every mod in the suggested factions list of SS+, along with SS+ and Nexerelin, so expect great variety)
3x capital:
1x Astral-class Carrier (the heart of the fleet),
1x Monolith-class Mobile Autofactory (Citadel mod, autofactory works like an up-scaled mobile HQ from SS+, which is itself up-scaled from the mobile resupplier. It also comes with a repair gantry),
1x Paragon-class Battleship (Heavy hitter of the fleet for when it's needed)
1x destroyer:
1x Hydra-class Boarding Destroyer (Scy mod, self-descriptive in role)
4x non-combative:
1x Prometheus-class Tanker (Gas, gas everywhere),
1x Eschaton-class Superfreighter (Blackrock Drive Yards mod, replaces my Atlas, more beefy weapon wise, but slightly less overall capacity at 1500),
1x Construction Rig Auxiliary (To supplement the Monolith after heavy fighting),
1x Locomotive-class Heavy Tug (SS+, like the Ox, but can haul 4 ships instead of 1)
16x wings, ~56 craft at full strength:
3x Xyphos Heavy Fighter wings (These suckers will go toe to toe with frigates),
6x Wasp Light Interceptor wings (The fastest and most numerous of my wings, good for most general purpose duties because of their numbers),
3x Skinwalker Space Superiority wings (Shadowyards mod, these guys eat other fighters for breakfast),
2x Kobold Support Fighters wings (Shadowyards again, usually assigned to my Astral to supplement the point defenses),
2x Teuton Smiter bomber wings (The Knights Templar mod, these guys will one-shot an unshielded Onslaught, they scare me when I have to face them in combat because I'm afraid I'll lose capital vessels to them)
Generally once a fight gets going, my Astral's decks are constantly abuzz with incoming and outgoing fighter craft, and very few fleets less than 30 vessels can stand against it simply because of the sheer number of craft. I've slowly built this fleet over time, and have been able to keep most of my progress on it thanks to the save converter. The Teuton wings were the hardest to procure, as anyone who's played with the Knights Templar mod knows how god damned powerful they are. It works quite well but is very logistic heavy, and running out of supplies is a problem I've had when dealing with extended deployments, not being able to fully restock and thus suffering shortages in important areas. That's my fleet, feel free to pick it apart and show me the inefficiencies (beyond the fact that for most people it's prohibitively expensive to use).