For the player-controlled flagship, I've been messing around with:
5 Light Needlers on the forward smalls
2 Heavy Autocannons on the forward mediums (can also use Heavy Needlers instead)
2 Flak Cannons on the inner mediums
3 Hephaestus on the larges, manual control (rest are on autofire)
S-mod Advanced Turret Gyros, Armored Weapon Mounts, Heavy Armor
Also have Ballistic Rangefinder, Hardened Shields, Resistant Flux Conduits, Shield Conversion - Front
Max vent then rest into caps (27 caps, 55 vents)
Skills are CE, IM, FM, TA, BM; TD, CM, CT, OT, BotB; Nav, GI, EWM, FR, CA, elite as applicable
Against double Ordos it does slightly worse than flagship Onslaught, but it does fairly well. The anti-shields are good enough to stand up to capitals, and the 3 Heph kill off pretty much everything pretty quickly. The 2 Flak Cannons are pretty much sufficient, along with shields. I run in, kill a few ships, then back off and vent, repeat. It also works to throw in some Swarmers just to help clear out trash/fighters early on, but that is at the expense of caps. I could probably get better use out of Harpoons, but then I'd have to manually control them and that's too much to bother with, so the Swarmers are simply always-on.