Mmm well yeah, even with SS+ pure fighter fleets do have issues end-game, but the thing is that's not how DA fleets are supposed to work.
Wanzers are not supposed to operate in a vacuum, and once the deploy cost is commensurate to the combat ability of the ship we can actually operate in the ship + cover doctrine while hitting the deploy cap - that's just not viable atm because of the deploy costs we've been discussing.
Certainly its already competitive in the mid-game when you're not hitting the deploy cap and you can over-deploy on DA ships.
I'm not sure what values Tart will settle on but some quick testing says once you can deploy Gusts in number and not gimp yourself firepower-wise, the battlespace changes significantly. Suddenly all the wanzers have anvils to hammer enemies against, and you have an over-supply of fighter bays to boot.
As far as Templars go ... well, DA fleets depend on fighter cover, have poor PD, and their abysmal shield damage/flux ratios means they can only pressure when they themselves are not being pressured.
Templars are essentially the perfect hard counter to that set-up.
In no way ever is a DA ship capable of shooting down a CLARENT with IBIS and RAPTOR weapon systems, and Burchels are generally too expensive OP-wise to fit everywhere. They can't counter-pressure effectively, and Templar PD slaughters Wanzers. Not to mention Teutons are essentially immune to everything except Burchels and massed Valiant fire as the poor projectile speeds on primary DA weapons makes them unsuited to hitting fighters. Hexafire and micromissile spam helps with the latter somewhat but you're still at a disadvantage.
No way to change that without completely changing how DA is structured
In the larger campaign sense there's still other issues - others have mentioned it; AI DA fleets, especially the smaller ones, are crippled by their reliance on the DA combat freighter, which right now is a liability in combat, and nearly 1/2 of the ships being suicidal in the AI's hands doesn't help any - but well, best not to change too many things at once anyway.