Hey, meant to get into this discussion a bit earlier, but I wasn't able to get this ready before then.
A couple of thoughts on how the battle UI works. Filtering is one of the major issues of this UI.
Here's a mockup, showing how I'd handle filtering and organize the whole a bit better.
Top left allows filtering Friendly Ships, Enemy Ships, Missiles (missiles would have visible trails to give origin data better) Fighters, Asteroids, Clouds, Hulks and Objectives / Planets / Something else.
Note the change to the orders; I really don't think orders should ever go over the main display and on most resolutions, we have room to burn there.
I didn't include Groups (which I doubt 1 in 100 players even knows are a thing, let alone uses) and the one major feature I still wish this menu had: the ability to give a Group a Formation.
[EDIT]
A few other thoughts.
1. It's not actually necessary to have the big selection-boxes around the ships, if the mouse isn't over one. It just adds visual clutter.
2. Honestly, I'd prefer to have 2 filter modes for ships:
A. Classic mode, but without the boxes- just the ship silhouettes in the friendly / enemy color. Most players will eventually just see the silhouette and be like, "hey, that's a Condor".
B. Symbolic mode, like the Navy actually uses; simple symbols for FR, DD, etc.
3. I think that either mode should always show the bottom of the icon in the direction of travel. It should be totally obvious what a ship's facing is, in this UI.
4. I really want the missiles to leave a fading track on this UI. Yes, it'll be a mess when it's all on, but it'd be soooo useful. More often than not, I don't care (much) about some random rockets getting shot at my far-away Destroyer, but if a swarm of death-missiles come out of the LOS fog, I sure want to see where they were, visually, so that I can properly intercept the source.
5. I think Groups should be explicitly shown to players, if it's going to remain a feature.
6. I would love to have a Patrol order, that takes 2 or more movement points as input.
7. I still think the game needs tactical formations other than "vague delta" and "just blob".