They are plenty balanced. The difference is how people play. Fleets don't get maxed out in typical MP games. But try to deal with 100+ bombers/fighters without a few Flak Bursts from Kols, and try keeping your level 10 capitals alive in the end-game without Dunov's shield restore.
The vast majority of the existing capital abilities have a good use, just that some don't come into play because people play short games.
But what of Vasari? I play big single player games like you and there is only 3 caps I would say are deffinates. The Egg, you can never have too many. The Seige cap because of how it is the ultimate vs a Star Base and for clearing up planets and the Carrier cap for obvious healing + strike craft boost.
But why bother with the Marauder? If I have about 5 caps already sometime I might get a Marauder to get a speed boost for my fleet, but if I use the level 6 ability of it once in a game that's more than I expect to. I often don't bother with the fleet speed boost, I'd rather just have another Desolator or Evacuator.
And what of the Battleship? If you are going to say the strike craft silence is so amazing then you just wasted most of the caps dps and tanking ability aswell because you don't have enough anti matter for Power Surge and the Silence ability. And the level 6 ability? Well I'd rather have Nano Disassembler, you get tons more damage out of it considering how cheap it is and it's short cool down. I do get one more than I do a Marauder but I just wish it was better at it's job, I wish there might be a reason that more than 1 of them would be useful.
Currently a Vasari cap combination (for 1 fleet*) consists of
(unlimited) Space Eggs
below is optional, more necessary on big games
(unlimited) Desolators but no need to get more than you have Space Eggs
below even in a big game it barely matters to get them
(optional 1) Battleship
(I'm mopping up so who cares now, I'll take one just for fun) Marauder
*With Vasari I tend to have 1 offencive fleet and 1 or more non cap defencive fleets that supports my Star Bases.