Oh christ, hyperions are irritating since the combat abilities update. I could see a fleet with every ship being controlled by humans actually being able to beat one, but even so, I think the phase jump thing needs to be gimped.
I think what bothered many people about this update, including myself at first, is that old tricks to rush into a large fleet were no longer viable with the supply changes. My strategy was always to get a venture as soon as possible, and then a bunch of wasps and broadswords to do most of the work against small fleets while I save for an Apogee. But between the supply restrictions (expensive supplies and being horribly imbalanced against fighters, but hopefully liable to change) and stricter early requirements for logistics skill, it's difficult/impossible to actually succeed with a shoestring cruiser fleet.
Personally, I've always hated the beginning of the game, and would prefer the option to start as a larger fleet to skip the worst of it (thank god for savegame editing). It's not that frigates are particularly bad, it's just really annoying to have to spend time pinging at pirate buffalos before the real game starts. I've never digged having frigates in a fleet, since they're so liable to die quickly against large and powerful fleets without babysitting, though admittedly I haven't used one in a fleet for years, so maybe that's changed.