I like how almost everything said here is available in halo ce and halo custom edition. You CAN fly other ships like pelicans, you can change what the guns shoot. All of this available through wonderful modding and downloadable maps. The only thing it lacks is good graphics.
But for halo 4...
i would want the armor to mean something (this was mentioned above and i am agreeing) this would make it more like a class system which people are familiar with. this would give the gave more depth and add complexity to it making your achievements count for more than your looks.
more tools like repair things and such maybe even anti vehicle mines
customizable weapons like CoD and maybe bigger maps so there could be 32 or more players