Naboo Infantry. Standard brown suited personal guard of the Queen. Naboo Guard blaster (similar to ST Rifle), blaster pistol, Repeater. Big bacta, heavy armor/high health.
Naboo Special Forces (Captain Panaka skin). Different looking uniform (with standard helmet in different color). Merr Sonn, ST Rifle, Pistol, Thermal Detonators. Slow, weaker as usual than assault in terms of health/shields.
Naboo Demolitions Specialist. Tempted to make this Jar Jar, but he doesn't really seem to fit in the scenario, so probably just another Naboo uniformed guy (maybe no helmet this time) that's different colors than the others, carrying Trip Mines, Det Packs, Thermal Detonators, Assault Sentry and Stationary Shield.
Naboo Pilot. Standard Blaster pistol and fists, plus Disruptor, Demp2 and seeker. Cloak?
Palace Medic. Heals teammates, repairs equipment, gives ammo. Possibly one of Amidala's Handmaidens (just for varieties sake). Standard Blaster pistol and Stun Baton (instead of melee), Demp2. Seeker, Bacta.
Qui Gon or Obi-Wan (not sure which). Standard powers, although possibly more Force variety (defensive Light Side) than Maul, but probably less health. Single saber with all three stances at least.
Feel free to throw out suggestions, obviously tweaking of the options would need to occur based on the level.
I don't have any plans right now to make this, just throwing out ideas.
An alternate scenario could be done around Capturing the Viceroy (very similar, but have the Naboo attacking, the Trade Federation defending). That would make more sense having Gungans or Jedi in the scenario as well, but might rule out having weapon weapons and emphasize stealth more.
As far as ammo is concerned, I figure there could be various "storage lockers" with Shield and Ammo stations in them. These would be inside the palace mostly, to force the attackers to rely on their Techs more.
Perhaps to balance it out a little bit more, the Handmaiden Tech could drop health packs (heals 20 each, recharge rate similar to ammo drops). And these wouldn't be usable by Battle Droids (but Darth Maul could sneak in and grab them if he wanted to).
The Trade Fed tech would have to actually walk up to his teammates and hold use to "repair" or heal them.
Oh and if a grappling hook is ever made for JA (ported from Q3A?) it could be given for the "Ascension Guns" that the Assault class would have on defense. It could be used to get from one floor to the next faster (like they did in the movie) or lay an ambush.
Additionally there is a brief shot of an armed Naboo speeder using its cannon to take out a Droid Tank (weak tank?!) and provide temporary cover for the Naboo troops coming to break into the palace to capture the viceroy.