(there's no other decent way to deal with tons of bombers at that point in the game)
TK push does a fair amount of damage and disrupts bombing runs...I'd argue it is better than flak burst, even if you include double taps of the abilities, but that's just my opinion....
In general, the carriers and colony caps are the best, with all six of them fielding very powerful abilities (like malice) or abilities with high utility (like ion bolt)...good rush players may start with a marza or vulkoras to hit an enemy HW early, but that is a big risk that may or may not pay off...
As Wrath said, sometimes marginalized capital ships can serve a purpose late game...flak burst becomes an enticing reason to build Kol's late game due to the number of bombers; detonate AM is one of the most useful abilities in the game and can justify the construction of a Radiance...
Two capital ships I would also seriously consider are the Kortul and Rapture....I'd argue these are the two best caps other than the carriers and colonizers...Kortul has 3 very solid abilities, and the vertigo/concentration aura is a good combo on the rapture (do not underestimate these two abilities)....
Revelations, Marauders, and Dunov's are probably ships to avoid until later on in the game....it's not that they don't have their uses, but they only fill very specific roles....