Much of this can probably be done with upgrades to the current version but here goes...
Maps with much more of a variety of air fields like some of those we see in FSO.
More variety in towns (not all towns the same)
Players pick their own spawn points for GV's
Bombable bridges that cross water with strategic GV spawns, maybe even rivers / bridges that divide towns
Other, more interactive terrian... trees that get run over and blown over, tank carcuses littering a battlefield, buildings that blow up in different ways, craters you can actually drive into, etc.
All acks are mannable and operate unmanned when not manned.
Fuel can be bombed to 50% (25% from the old days was too far but I think 75% is not enough)
bombing a % of the barracks or ordenance on a field has an effect on the number of troops, supplies, size of bombs you can take, etc.
CV's where commander can disable flight
NME bases flash when a CV is shelling town (a single jeep 3 miles from a base will flash it but not a CV that is actively shelling it? Makes no sense)
Allow players more tower functionality while in flight for those long boring flights (look at and select skins, convergence, armorment, performance charts, O-Club functions, etc) Of course any changes made would not affect the plane that is currently in flight.
Make it so joystick inputs dont effect a plane while in stick calibration mode.
Add function to allow players to switch from one individual sound pack sound to another while in game... and the ability to listen to each sound while in game.
Alow players to turn off their transponder (or mission ability to turn off transponder) so they dont appear as a radar dot to friendlies
How about perk points that buy extra cruisers or carriers for a CV group.
Additional radar towers that are not located on bases
Revised CV / port mechanics where cv's spawn at an interval (can be scaled based on number of cvs the country holds... ie first one in 10 mins, 2nd in 30, 3rd at 60, etc.) Ports dont wait for the old cv to die to respawn a new one after capture. When players destroy a ship docked at the port, it affects how the port spawns a CV.
Make 1000lb and larger bombs cost bomber perk points
More Skins, More Maps
Maps that only rotate weekly, maps do not switch after reset. (we miss the fun of some of the smaller maps because they reset easy)
Better Tank Towns, more tanks
Vastly improved graphics on the ground would also be nice. (is it possible to have two different engines for the same game? one for the GVers and one for the flyers?)
I wouldn't mind seeing a part of the game as a free first person shooter (pay to fly or drive). Would be interesting seeing a player driven m3 dump off a bunch of players armed with a variety of weapons and explosives, buildings that you could go into, attack or defend, gv's that you can jump out of, you could make it so you need to drive a jeep (or run) from the tower to an ack position if you want to man it.