First and foremost: this is a non-canon issue.
You were warned.
Let's use the Galaxy with saucer separation ability as example: in STO the standard saucer is something like a big engineering module, with two phaser arrays and some minor hull and shield healing capabilities.
I wonder: why the Starfleet Engineering Corps has never introduced more specialized versions of the saucer? After all the saucer is infact a bigger and independent version of the Nebula's pod.
Tactical Saucer: a small and nimble saucer equipped with two arrays (one fore and one aft) and a dual beam array (fore), with the "Beam Array: Fire at Will" feat, but fairly weak shields and hull. The saucer of choice for any battle oriented mission.
Scientific Saucer: not too small, not too nimble, not too shields and not too hull, with the standard weapons (2 arrays) but many scientific feat: the saucer of choice for any exploration and support mission.
Carrier Saucer: a basically motionless saucer with good shields and hull, with some point-defence weapon (one or two phaser turrets) and the ability to launch "x" Peregrine Fighter, or Danube etc. Basically it is a little outpost.
Siege Saucer: another motionless saucer, with fairly poor shields and armor, but with good point-defence weapon and especially a starbase-sized phaser: something between a guardian satellite and a big sniper rifle.
Needless to say, these saucers can be bought at the C-Store.
For our brothers of the KDF a new ship (Klingon, Gorn, Nausicaan or Orion, as you wish) should be developed and then sold (along with its... "Saucers") at the C-Store.