Armor won't work on troops, so your idea of Bounty Hunters/AT-STs/etc get damaged first won't work.
Ion Cannons are not simply anti-electronics weapons, for as far as I know they're just heavy weapons that can be mounted on fighters.
http://www.starwars.com/databank/organization/ for a LOT of other troop types.....
The same Databank has a lot of info on the Yuuzhan Vong, they use a lot of organic technology. Also, the Databank has enough info to keep you modding for months.
You could create Neutral races like the Naboo, Gungans (yes in the Expanded Universe it is said they made the leap to space), Mon Calamari, Bothans et cetera.