So general thinking I've been doing...
I think we actually want to limit the number of our active military designs, and try to avoid overspecialization.
One reason - keeping a core of ships that can act independently, and don't need each other to survive - has already been given.
The other is one of resources. Not duranium and all that, but another key resources - shipyards. We only have so many of them, and while we can shift retooling them around as needed to face crisises, this can bite us in the (shiny metal ass) if a situation should develop where we face an urgent need for ships of a specific type, and need to wait months to retool the necessary shipyard (which may in turn bite us in the ass if we need two such).
That lead me to conclude that we should build the core of our navy around one multipurpose workhorse - not the three we currently have (Battles, Stars and Attitudes). This ship should be able to carry out operation in small groups or even alone, to provide defense to less critical star systems in the later game.
In addition to this shoudl be what we build into our main battle fleet - I think the consensus is heading toward making that a carrier fleet. This means one standardized model of carrier, as noted above - one role one class one shipyard. The independent combat unit can be used to reinforce the carrier's escort, of course.
Anything beyond these two units should be role-specific, eg our already-designed PD unit (anti fighters/missiles escort for the carriers), monitor (planetary bombardment) and combat direction ship (until we can fit satisfactory detection and fire control equipment on the carriers and main combatants), Spies (recon) and whatnot.
Of course, I'm not criticizing the current division, because that's a necessary effect of our slowly developping capacities - no point keeping our main combatant at 8000 tons when we can reliable build at 12 000 or higher. I'm just proposing what I think should be our aim.
Yes... one complicating factor is that neither our tech nor our shipyard capacity will remain constant. Tech advances are useless to us unless we translate them into ship designs and then actually build those ships. This, taken together with our desire to retain our experienced crews rather than break up old ships, leads automatically to a variety of designs of different classes.
The situation will grow esaier as we build more shipyards, which is one of the tasks that I intend to undertake once our resource situation is solidly in the black.