OK, I've taken a brief look. Looks to me that:
1. The current combat UI element that handles Flux / Hull (the widget just off of the ship) could be rescaled based on screen footprint without serious issues.
2. The aiming guides don't scale well at all. At 1600/1200, they're pretty hard to see and at high zoom, they're obliterating details. This is a tricky one. Maybe have the active guide pulse gently into out of transparency, so that it's easier to see?
3. The bottom-left UI can probably be rendered to an element and scaled, but it's quite a lot of screen already.
How much of the information needs to be in that corner? Is all the text really necessary?
Can't the ship-damage display be moved to the top-left corner and the text scroll be moved to the center? What about the complex UI listing system for all of the nerf/buff? I feel, pretty strongly, that when all of the complex mechanics need all this space to be explained, maybe it's time to think about whether or not to allow users to selectively turn it off.
I tend to not notice the sheer clutter at this point, but I'm sure newbies feel overwhelmed, and at high resolutions, they're probably squinting a lot (and dying as they lose focus).
The nerf/buff UI, in particular, feels like maybe it could be an element that minimizes unless something has changed recently. Maybe, at the start of a battle, flash it centrally, then tuck it away unless conditions alter substantially?
4. The System timer bar should probably be on the central widget, rather than down on the lower-left UI. It's that important. I think weapon reloads for anything that takes more than 1 second to reload could be there, too (average the values or just display the weapon that's closest to reloaded, maybe).
5. I'm really not sure why we need a complete breakdown of all of the weapons in each Group. We set the Groups up, after all, and we should know what's where. At the very least, there's something that I'd definitely make an optional display to free up space. At the very least, hide it until we switch Groups.
6. The weapon refire timer UI feels like it could be way smaller. Perhaps weapons should get a short abbreviation string, limited to 5-6 characters, so that it can be compacted?
7. The ship damage display only needs to render briefly when we're actually taking hits, to actively inform players that they're taking damage and how it's impacting their Armor, etc. It can get moved to just-below the Command Points / Deployment Points display (but, frankly, why do we need those on the main combat UI at all, when we spend those points in the Tactical Command UI?).
All of this would free up space, de-clutter the UI and allow for scaling without being a total dumpster fire, I think. Most of this involves moving elements, or not drawing them unless <some event>, rather than writing whole new systems, too.