I like these ideas, I'd like to see the resources used better, Starships are made from metal, so it should take ALOT of metal to build them. And a small amount of dilithium to run the ship. Maybe you could scale it so that each ship you build, the more and more dilithium is needed to mantain your fleet.
Latium should be used for trades, and research only.

That is just like star trek.

PLEASE bring planets back !  But make them usefull. have speical ability things that can only be researched on planets.  Like Crew heal rates. if you research on different type planets they yeild different results.

Orbital space docks, Defense platforms, Outpost stations are KEY to holding your planets. There was a great orbital system put into Armada 2, i remember when the game was being made, Requesting it to the makers on there fourm, And my wishes was answered. We should return to there usage.

Instead of working on ALL races at once, to speed up FO development, just work on Alpha quantrant first, then Beta, Then Gama, Delta untill the entire galaxy of races are completed.

Maybe have a Fleet Ops mod editor so you can swipe out newer ships with older ships. So it could be easy to build a custom fleet ops game.

AI

A.I. is the MOST important thing. It needs to be tough. It needs to fool me into thinking i'm playing another person. CRAZY A.I. like sucide raids, and charging,

Gathering resources should NOT be a threat. Building a Fleet of 25,50,100 ships should be !

I usaly build 5 fleets of 16 starships each. and lable them fleet 1 to 5. Then when i'm done toying with the A.I. or i get bored an want to end the game i send all fleets into the enemy's base in One massive attack that leads to victory. I've seen the A.I. do this also to me also. And these was Akira ships, This was in Armada with Warp enabled. I think sum ships should be able to warp. like scouts.

Phasers beam width is too large. it needs to be scaled.
Move during battle should be default to on, it's so dum to have your ship just sit there.

Scripted battle moves. THIS would be Awesome !

Lets say you have your Defiant class starship & 5 scouts in diamond formation against 1 borg cube. instead of circling around the cube, or standing still firing at it. Your ships really fly around it in a random sctiped move around the target. ( Like all the lil ships in First Contact, how they all buzz around the large cube and attack it. )

I talked about this in another post about battleships.

The amount of battleships should depend on your fleet size. for every 10 ships there should be 1 battle ship. So a fleet of 100 ships, you would have 10 Battleships this should even out the game play and not allow the A.I. so build massive battleship fleets.

That's all i can think of right now.

i dont' know the inner working of the game well enought to come up with a solution. but i could guss maybe scripting the attacking target as a orbit point sumhow. And then the scripted battle orbit manuvers would run after that. You know how you set a mining colony in orbit of a planet. make that orbit path set on your target sumhow. And then run a pathing script that makes your ship bank and turn towards the target and randomizes the path between a few scripts so it looks kinda natural.

You have to think outside the box. in TOS.. you would see ships stationary and firing. In TNG ships would pass by eachother on a run. in DS9  DW ships did all sorts of moves. There moving things. they don't just curcle a ship, then use all 3d vectors in battle. like the Defiant & Lokata, flips, passes by, banks turns, nice and active battles. These of couse are for small scale battles, but massive scales battles would be different. With ships holding the lines far back. and smaller ships attacking.

just so you know 90% of this stuff is all ready on the fleet ops staff to do list and allot of the ideas they have already said no to. Planes for instance...why would you colanise a planet in the middle of a war zone it just doesn't make sense.