I had a few ideas for units and rules tweaks that could bring a few new twists for someone's customized setup.
Flagship - A seagoing variant on the General unit; its destruction loses the game for the owner. Not sure what its stats would be, possibly that of a cruiser? A regicide scenario might use only one or the other, or each player might be given a choice of whether to play as a "Marshal" or an "Admiral" at the beginning of the game. Perhaps a scenario could be set up so everyone starts with one of each--in other words, you have to lose both your army and navy command units to lose the game.
Transport submarine - trades most of the offensive power of a "killer submarine" (backronym) for a modest cargo hold (1 or 2 slots max). It should only be able to carry a handful of unit types: infantry, engineers, and recon[see below]. Transport subs could be used to mount sneak attacks behind enemy lines, or to convey basic infantry or engineers through a hot zone too dangerous for transports.
Should a transport submarine carry a General unit? It would allow a nice option of getting your General unit to safety if its resident landmass were suddenly surrounded, though in the interests of fair play it will probably be necessary to let satellites detect even deep transport subs, to counterbalance the obvious "underwater undetected general" tactic.
It's also awfully tempting to have a transport sub carry and launch satellites, short range missiles, and short range nukes...a quick nuclear decapitation attack on a newly-located General would be a pretty impressive way to win a game.
Recon - A land unit with the same stats as an infantry, but has 5 movement per turn and can enter any terrain an engineer can. Recon units are visible only to other recon units and satellites (one more reason to build one); anyone else only detects them if they run into them--and if you don't kill one after spotting it, trying to track it down is going to be a pain. Recon units should have the same build time as an armor unit, fight like infantry, but cannot capture cities or convert to other units. Recon units would fill the same function that destroyers and fighters tend to do: exploration of neutral or hostile territory. While efficient, throwing endless waves of fighters against an enemy's fighter-defended frontier seems less elegant than using a few stealthy recon units (perhaps dropped off by a transport sub) to map out the interior of an enemy-held continent, provided of course that there's not a lot of enemy units wandering the countryside.
The following would probably require some modification of the code that computes a player's production efficiency, but here it is anyway.
Factory - A new stationary land unit that is able to build other units like a city, but does not count against your resource drain (nor does it help it) if it isn't building anything. A newly-built factory should have some begin with some very low PE, but this can improve over time if left idle. Should a factory be able to specialize? I'm not sure; maybe one could have a separate "specialist factory" unit which does this. Factories can only be built on clear terrain and should take longer than an Oil Facility to make. You would probably need a lot of Oil Facilities to support a large number of Factories. This unit is mostly inspired from the WW2 era of bombing an enemy nation's industrial capacity rather than going after civilian targets.
I imagine it would be a lot of work to implement these unit types in the the stock AI. More than likely if these units were ever built, they would be used only in PVP games, but I think they would make a pretty neat addition to the game.