The fact of T6 ships now being scaling, and usable from immediately after the tutorial is a good thing. However, there is one issue I can see arising: that it can be impractical to keep their 'canon' loadouts... for the Bastile, this would be Voth-AP arrays and their
transphasic-chroniton torpedoes. Sure, you can search the Exchange for the arrays, but this can be problematic for things that aren't the flavor-of-the-month. So, I found myself asking, what solution can be put forward wherein everyone (or, at least, almost everyone) wins?
I think the path to such a compromise comes from the Andorian escorts - specifically, how having one commissioned (whether active or in drydock) comes with the ability to requisition the complete range of Andorian phaser weapons from the dilithium store. Just apply this rule to
all ships with distinctive weapon flavors; these weapons would be freely upgradeable to Mk.XII (if this is the case for Andorian phasers or spiral-wave disruptors, please let me know). This would one, increase the desirability of their associated ships; and two, requisitions and post-Mk.XII upgrades take more dilithium out of circulation. Desirability of said ships would be in my opinion further increased by giving them the extra mastery tier (6 - account unlock) introduced with the JHV ships, but that's also a conversation for elsewhere.
Would demand for the versions that come out of the various boxes ending up on the Exchange be negatively impacted? Not really, I think.
Sort of related would be the case of Dominion-polaron weapons (mission reward choices from
'Boldly They Rode'. An argument can be made for not only expanding them into a complete family (adding dual-beam banks, dual heavy cannons, and turrets), but that they should be the ship weapons offered by the Dominion liaison that becomes available after completing 'Scylla and Charybdis' as well as the default weapon type for Jem'Hadar characters.