I understand the units are supposed to fit certain roles Blair, the only problem is that one would think Cruiser's are supposed to be a little more effective in combat than a frigate.
I don't know if this makes sense but here is my take on the issue.
Frigates - Very specialized roles: Such as combat, fighter defense, colonization etc...
Cruisers - More powerful specialized ships: Good at combat but also have a few abilities.
Battleships - A truly multi-role specialized combat ship: Dish it out and take it too, as well as having many varied abilities that make them the heart and sole of a fleet.
It just seams, And I don't mean to be offensive, that cruisers as they are now are a waste of resources. Better spent on Cobalt or Missile Frigates. Tho the Kodiak is good to go with a little boost in its intercept speed.
In the Sins Universe, which is probably different than those many are used to, Cruisers are more like middle level commanders that perform higher level tasks and let the grunts (frigates) do the majority of the dirty work (fighting). They were intended to be escorted around and in combat to sit a bit behind the main lines supporting and enhancing their troops. The Kodiak is the only one oriented around combat and even still, his role is more of a meat shield than damage output per supply cost. e.g he can take a beating while suffering attrition from long range LRM's
Given the correct fleet layout, a fleet of frigates properly supported by cruisers will decimate a much larger frigate only force. Obviously, the system still needs balance but the philosophy is that cruisers are not, in and of themselves, oriented towards the dirty work of combat.
Edit: Naturally, if this is not working we'll have to reevaluate as per usual 
