Perhaps making some era advances / regressions with ground units? I would suggest the bipedal war droids for the empire (era 3) that are present in Dark empire 2, but I'm not sure if they would be difficult to animate.
I presume the team doesn't want another "tank" for the empire then. As good as the ATAT is, there doesn't seem to be any heavy imperial unit with all-round firign arcs. Maybe that's the intended achilles heel for their army. If not, might I make a suggestion for them for one last tank unit?
One small idea was a new gc in which the NR had a line of planets leading to a line of imperial (era 3) planets (or a rough corridor). If its not too difficult to code (probably is, but I might as well suggest this) have a structure in orbit around byss at the end of the imperial corridfor in the shape of the galaxy gun. This produces warheads (so its just a large shipyard) which cannot be seen anywhere except on the gc map. they are also unkillable and cannot be interacted with except by the empire player on the gc map. Said warheads can be sent to an NR system and be used in the manner of the death star in the original EAW, destroying the system. What makes theme different is that they are expended upon use. Essentially the aim of the gc is to fight your way by hook or by crook to byss and destroy the galaxy gun factory. the empire player has to defend whilst having the option of using these (expensive) warheads to destroy NR held worlds. I'm only suggesting this for any perceived novelty, and it would be a one-off gc. Otherwise, its just a useless superweapon that has no place in the mod.
I might perhaps suggest the use of world devastators as a kind of mobile mining structure- place above an enemy world and you get a small cash bonus per turn. The NR would have to drive it off to reduce the funding the empire gets (they are taking resources after all). nothing else and hopefully nothing fancy. Same as the above however, this is only a suggestion and intended for a unique era 3 unit- NOT a silly all conquering superweapon (having played all the command and conquers up to RA3 I have good experiance of how annoying those things can be).
As regards missions- I'd suggest an ambush of rogue squadron by the corrupter at alderaan for isaard's era. Take rogue squadron to alderaan (or the corrupter if you are the empire) and fight the empire with that squadron and maybe two more x-wing squadrons. discover and capture the alderaanian war frigate if you scout around to even the odds. Victory comes when convarian is killed or driven off- empire forces would be the corrupter and an extra interdictor cruiser.
zsinj era- razor's kiss mission, already suggested.
daala's era- take the knight hammer to yavin with a ground force, where there could perhaps be ground forces made up with slightly more powerful jedi than usual, but nothing else. Eliminate them to win. The NR mission for this would be to take han, luke etc there to the ground and have the imperials launch a ground invasion. fight them off with the extra jedi to win.
era 3 might perhaps see (as a mission) palpatine ordering the assault on new alderaan- a straight up ground assault with only the resources he gives you. empire attacks, NR defends.
pelleaon's eras. send three star destroyers through a secret route to mon calamari, attack any NR forces there. perhaps give them cloaking devices like in the hand of thrawn duology for this single mission. the NR mission is to be surprised by them and have to fight them off.
The empire of the hand mission in that gc would be to send clawcraft squadrons to various locales, and "buzz" IR/NR craft to gather intel on them. Completion of this (and bringing the surviving craft home) perhaps merits extra cash or gc map intel.
I have some ideas for the PA, including a "what if" tech level advancement- perhaps a craft or two could be introduced in eras 3-5 and the description being "Khaine's engineers were on the verge of introducing vehicle X before shadow hand and the upheaval of khaines death forced the design to be abandoned" or something. Perhaps, in the same way that the empire have novatroopers that can be built only twice, the PA could have the Nemesis gunship from The Force Unleashed- can only be built twice, complements the LAATI but is horrendously expensive? Just a thought.
http://starwars.wikia.com/wiki/Nemesis-class_gunshipAnyways, that's my two cents. Hope that proves a little useful.