For me, the only real advantage MOO2 had over Armada 2526/Supernova was ship design. Even then, it's not a feature I miss that much.
The tactical battles are not particularly done well. It just lacks the charisma that MOO2 had,
Honestly, I didn't find the battles in MOO2 to be any better. The whole bit about one side getting to go first made them horribly unbalanced IMO.
ORIGINAL: Gelatinous Cube
My biggest problem with Armada is the map. It's perfect, except that you'll go blind trying to differentiate who owns what. A mod for that would go a long ways.
Have you tried using the "show empire territory" feature on the mini-map? I've long found that to be useful in helping determine who owns what.
It's so blocky and hard to read, plus on larger maps the colors become redundant, and it's difficult to tell which colors are who. I love Armada with the Xpac, because it fills a niche in my gaming diet that no other game can--that old-school 4x feel with modern sensibilities. The AI is good, the coding is top notch, even the interface is great aside from the whole not being able to differentiate empires easily enough.
It's a big enough problem that I would actually pay money just for a graphical overhaul, but not so big that it prevents me from enjoying this (quite good) game.