Myself, I'd like to see more variation and depth added. As Ramano said, it's close to Flashpoint as is now, which depending on your preference could be a positive, but for me, it's a negative. Flashpoint was show up, most guns wins. Little choice to be made other than where to go and when, and number resolutions painfully predictable.
Overall I much prefer the AE style mentioned by Hop, however that's not without it's weirdness and weakness as well. I do think depth and variation can be added without complexity. Part of the current lack of variation is that there isn't much room for tactics when things are set up for cap ship combat to be a melee. For starters, I think enlarging the battle grid, moving away from the strictly orbital/circular layout, add firing arcs for capital ships, limiting deployment of fighter/aux units, increasing ranges of weapons to allow for space between units and different tactical worth, and increasing unit movement to go along with that are good moves.
Regarding Hale's mention of moving to a system of grouping fighters one at a time, I really dislike that application and from experience it just creates weird dynamics. What you end up with is people massing a group of fighters with the specific number/values required to overpower an opposing group, which doesn't sound so bad in your head because essentially when grouping squads together you're doing the same thing, overpowering force to decimate, but when you can do it on a per fighter basis, it just makes the whole dynamic a little too weird imo.
Ideally though, I'd like to see a system that almost forces application of "Lines of Battle" that are depicted in WEG Sourcebooks and with larger fleets. Doing so I don't think would be incredibly difficult or hard to manage and would necessitate and go along well with enlarging fleet sizes, to the point where a player's fleet might look like 3 ISDs, 4 SRKs, 6 CRKs. etc. To do so, the 'presentation' of cap ships has to be reigned in a bit, almost treating resolution of combat between them similar to a system of Rating Comparisons and Potential Modifiers amidst starfigthers. Albeit with arcs obviously as a requisite to "lines of battle" styles of engagement. It'd take a bit of mocking to hammer out the kinks and identify holes though. For starters to instigate forming lines and such, you have to limit 1 Heavy Cruiser per Grid Space (otherwise they're colliding) The value system would have to be heavily worked towards smaller numbers, for instance. . .
ISD
SPD 5 (moving foward)
MAN 3 (change heading 90 degrees)
ARM 50
SHD 30
ATK
Front 12
Left 10
Right 10
Back 2
MC80
SPD 3
MAN 4
ARM 30
SHD 60
ATK
Front 7
Left 8
Right 8
Back 4
So imagine 4 MC80s going against 4 ISDs. Obviously, initially the ISDs are going to want to approach and maneuver to face MC80s head on one for one to get most of their front arc, however MC80s are going to want to line up and go broad side for broad side. The speed of the ISDs allows them to close quickly, but the better maneuverability of the MC80s allows them to adapt and have more changes of heading in order to maintain their lines, the ISD commander with more speed but less maneuverability has to decide to charge in disorganized, or form up in a line. Once they get in to exchanging blows, the low Man of the ISDs is going to make it difficult to get in order if they are already not.
Now, say with a range of 2 for their TL weapons (ratings), these two groups are formed up in the lines and passing each other exchanging blows. As the lead ship of either line passes the last ship of the opposing line, it can turn away from or towards the opposing line, potentially being able to get across the stern of the last ship in the opponents line for a clear rear shot.
It can be made to work with enough trial and error and finding the holes and plugging them. Just airing out ideas. The other nice perk with larger fleets of scaled down cap ships and more heavy ships means in a battle you could actually lose a couple heavy cruisers and the battle still wages on, rather than the usual dynamic of a heavy cruiser going down and the fight being pretty much decided.