Strengthened Capital Ships - Check
Stronger Star Bases - Check
Reduction of Bomber Spam effectiveness - Check
Hmmmmmm Star Bases are now a little too powerful. Only Vasari has effective weapon. Hmmmmm. Increasing weapon effectiveness of Anti-Structure vessels will not be enough. Its time for abilities.
See? It got worse.
You could give the anti structure unit for TEC and Advent an ability that fires something like the demo bot. They launch a torpedo that disables weapons for a short time (like it disables for 3 seconds and has a 15 second cooldown so you must have 5 or more for a permanent shutdown).
Or go a completely different route and have something that weakens the shields and hull so that all hits to the starbase count for more while the ability is active. (And make it a close range thing... So the structure has a chance to kill what's weakening it.)
And worse still.