First, let me introduce you to the game itself:
Battle Engine Aquilia [http://www.youtube.com/watch?v=6mMta1GrSgM]
This game came out for the PS2, PC, and IIRC, the Xbox. In it, you play as a Humongous Mecha fighting in the middle of a war zone. While you carry out your missions, the battle rages around you. Your actions turn the tide of the battle, and can even help you at times.
Enemies range from tiny infantry (you can't stomp them, but blowing them away with your landing thrusters is just as fun!) to tanks, turrets, aircraft, Naval vessels, and giant superweapons. Your machine has a variety of weapons, and can change into a flight mode to battle airborne enemies or strike ground targets from above.
The game's only drawbacks were a low budget, and the problem that your mech can't handle water at all.
Anyways, a sequel would change that part immediately. In fact, out of the different Battle Engines, amphibious machines would be available. Other machines would have well-defined operational parameters. Some would be built to fight best on land, some on the seas, and others in the air. Within that, you'd have bomber types, Artillery types, Frontal assault types, and the like.
Also, improve the army AI a bit, so it can fight for itself more on both sides.
The idea of the Wingman you get could also be expanded. Your first few missions are solo, then you get a Wingman, and by the end of the game, you're commanding a small squadron of fighters or a fireteam of Battle Engines.
Online play would be available: Cooperative campaign, free missions, deathmatches, and the like. Instead of weapons, you buy support attacks, like an airstrike, artillery, airdropping tank platoons, and even orbital strikes (lasers, Rods from God, and such). Missions and the campaign could also be played cooperatively offline as well, on the same system or on a second, third, or fourth.