The way I see it, this can be 'fixed' pretty simply.
1) Make the missile barrage effect more obvious (or is it just my screen that makes it look like just a bunch of javelis firing?), a shinier effect would be nice.... mebbe a larger fire spurt blasting out of the launchers or something. The sooner you notice it the sooner you can stop it, so less beaten people whining.
2) Buff the Vasari Marauder's combat abilities so that you aren't shooting yourself in the foot taking one early game just to have some protection against the Marza. Really, that thing has GOT to be the WEAKEST cap in game... and w/ the new Kostura in Entrenchment... it can be rather redundant to have one (don't get me wrong, the kostura gets you into nice places, and the Antorak gets you out of them, but, play your cards right in the first place and you won't be needing to get out).
3) Possibly give the Vasari another interupt ability. Does the Gravity Warhead interupt abilities? If not? It should. Everyone has a god damn space whale anyway. If it does, scratch this last one. I would LOVE some clarification on this, does anyone know if GW has an interupt effect? (LOL, I only use it when they are running away, so... never really noticed)
4) Increase the target cap on the Vasari Desolator, or remove it COMPLETELY. If the Marza can hit ALL targets within range, it only makes sence for a technologically superior alien vessel to be able to do the same with what is essentially the same tactic... Note: I do not think that the Desolator should fire WAVES. It should just fire off one spurt that hits everything within range, once. Failing uncapping the ability, increase the number of ships affected to somewhere between 16-32, seven is far too weak.
If you are playing TEC, or Advent, you really have alot of options to interupt the Marza, and likely need to pay more attention in battles... see option 1, a simple cosmetic fix (although, let me double check my particle settings, mebbe I forgot to turn something up ).
Anyhoo, as you can see, I do NOT advocate nerfing the Marza. I used to, but... I've realized that it's not neccesary. I also highly reccomend the AI be improved in terms of cap ship ability usage... as it stands the AI does NOT use interupt abilities effectively, and a Marza is just about an I WIN button against the AI after level 6.
I personally think that option 4 is needed regardless of comparison with the Marza, as the PMS is weak. And you would rather think something called PMS would be far deadlier than it is... I mean geez, the average girl friend's PMS has no target cap and issues 1,000 dmg to each target (and it bypasses shield mitigation) and applies the "Migraine" effect, which disables the use of abilities for the duration and drains 200 anti-matter!