I don't know if Advent or Vasari players have similar concerns, but if they do, I would suggest these tweaks for them as well. I haven't played Advent/Vasari yet so I'm not familiar with the Rapture or Antorak. One day.
The Antorak is right up there with the Dunov as one of the game's most marginal capital ships. The Rapture is
highly underrated and is extraordinarily powerful. Large Advent fleets should
always have one.
Really, autocast is an issue, but the bottom line is that the Dunov's abilities just aren't that strong. Shield regeneration in particular is one of the least impressive abilities in the game. The Dunov's EMP is probably the only reason it ever gets built in competitive multiplayer.
A good starting point would be to allow shield regeneration to self-target. This capital ship has very low combat potential but its abilities demand that it get very close to the enemy in order to be effective, putting itself at great risk at all times. The Dunov really needs the capacity to defend itself, so I feel self-target is a must on shield regeneration.
Secondly, shield regeneration really needs a secondary effect. As a single-target ability it doesn't scale effectively once fleets are no longer tiny, but due to having very poor combat potential the Dunov isn't viable early-game, so the ability is already largely obsolete once you have it. By adding secondary functionality to give it a more diverse effect, it can be applied in more situations.