There's a simple fix to this:
Give each faction a new frigate that is designed specifically for attacking titans and nothing else.
Make them cost half as much as a Titan.
Make them Kamikazi units that reduce titan shields to zero and HP by half upon impact.
Example: The Tec's could be essentially a Novalith Warhead atop a pair of phase drive engines.
The advents could be a small ship full of clerics who use their spiritual brain powers to make the Titan crew go mad and kill one another. W/e works.
Vasari's could be some kind of nanite swarm that enters the gravity well and eats away at the Titan's hull.
Make them slow, lumbering things so that either the Titan wielding player has to make a stupid mistake to hit it, or the titan killer wielding player has to use good strategy to get his titan killer into a position to ambush the titan. If you really want to make it challenging, give all titan hunters an ability that makes them invisible upon entering a gravity well for a short duration, and invisible to enemy phase lane radar.
Problem solved. Balance restored. Game fixed.
Disclaimer: imho 
Also, if someone wants to work this into a mod, that would be awesome. I really think it would restore a lot of strategy to the game.
Edit: It's also a matter of realism. There has never been a war that had a technology that could not be countered. Nukes will someday be countered and made obsolete. Don't ask me how, but they will.
