Sadly I find this true as well. Anything two or even three frigates can do chances are one cruiser and a fighter squadron can do it better.
The only exceptions to this are
1: Spamfests - Ion spam and plasma being the most effective. Ive seen challenges with incredibly huge blobs of frigates just steamrolling everything, at least the first few times you try it (then you have to switch to another spam type). Not very fun at all, and doesnt require much thought. (Biggest was 112 Imperial frigates with plasma and no engines, so much of the stuff that even my fighters were hit)
2: “Support” ships for your cruisers. As in, a wall of cruisers with anti cruiser weaponry, and maybe five to eight frigates with tractor beams, missle scramblers and anti fighter stuff following behind.
In short there isnt really any fleet where your main force would be frigates backed up by cruisers. Frigates are more fragile then fighters with potentially more destructive force but rarely do they ever get to use it because by the first minute mark their all torn up by fighters or missles. I know GSB isnt based on realism but it does seem a bit silly if your 50 tonne frigates with armour plating and shielding are dying to a couple of fighters in seconds.
I reckon that your idea is good Winter: introducing command and communication, repair and targeting modules that affect more than one ship could help to make a group of frigates stronger than the sum of its parts, rather than just cannon fodder. Rather than going for maxed out cruisers with fighters you might then consider using frigates more; for example instead of a group of six cruisers and two anti fighter frigates, you would use two cruisers, one with anti fighter and one with modules that boost the offensive power and accuracy of nearby frigates. Perhaps, escorts with target painters and cloaking fields, lighting up enemy cruisers for your own missle ships, then hiding.
Just some thoughts, I encourage any of you out there to post good balanced frigate designs and share your own strategies.