How about, making it into a sort of FPS, where you are a COveannt Elite, or a UNSC Marine, and you have other soldiers under your command, and you can order your soldiers around.
Every time you play, you are presented with a choice of different missions, and which one you take afffects the storyline.
You would be able to join a different group (such as soldier, spec-ops, command, pilot).
Your 'group' would determine what extra 'attributes' you and your squad get: a soldier would be stronger at normal combat, a spec-ops unit would get better equipment, a commander would get more and better soldiers to command, and apilot gets better vehicles.
Instead of classes (rogue, soldier, etc) you get several attribute points every time you gain a rank, and you can choose what skills to upgrade with these points, such as running speed, melee power, accuracy, etc.
You also get equipment points, which you can use to 'buy' new equpiment. You would be able to get better armour (which is heavier, and slows you down), better shields, better guns, better vehicles (up to a scarab), better soldiers (such as a hunter), more soldiers, or a (For example, there would be an advanced Active Camo generator, which is always on until you get hit, which costs a large number of points, and a basic Active Camo generator, which runs for only a few seconds. There would be different levels of active camo in between.)
You would also get mission equpiment points, determined by the type of mission, which you can use to 'buy' one-use items, such as orbital strikes, grenades, ammo, etc.
Eventually, by the end of the game, you would be commanding several hundred soldiers with the best equipment into battle, with large vehicles and spacecraft under your command, fighting another huge army. You would still play like an FPS, but you can pause the game, and command your soldiers wwhile in FPS mode, or switch to command (RTS) mode, to control your soldiers. (You would use RTS more and mroe as you get mroe soldiers)