It makes perfect sense that players should only be choosing one capital ship as their primary cap in a Real Time Strategy Genre.
It is exactly because this is a Real Time Strategy game that you should pick the Marza first. As Vasari, you should pick the Death Egg first. As Advent, you should pick the Mothership first. This is what you should do because it is to your advantage.
And if there's more than one significant battle going on simultaneously? Does the player essentially need to ignore all other fronts simply to monitor a single enemy capital ship?
You can choose to simply monitor the Marza if you would like. Preferably, just pay as much attention to it as you need to. It isn't hard to notice that a large number of your ships are suddenly blinking red all of a sudden. It also happens over 20 seconds. One MB is two clicks away (moving it into a good spot and then firing); one counter to that is also two clicks away.
I agree with Astax, if the Marza gets nerfed it will be tossed aside. Use a Marza against someone who knows how it works and it isn't as OP as you would think. Seriously, you should try it. It is frustrating, you are expecting awesome but it never happens. Which usually leads to you running away with it right afterwards. It takes effort to not get destroyed by it. In converse, it takes effort to keep it alive.
What would be kind of cool for the Marza is that MB is instant damage of 150 to everything and very low cooldown. Cast as many times as you have antimatter for. But seriously, it is fine as is.
Speaking of Novaliths...doesn't Auxiliary Goverment nerf that? Advent late game has the best fleet, btw. Shoot a culture cannon at any planet you are going to attack too and you erase their culture advantage there and you get benefits from your culture there.