great question;
for ultra large scale events, I've had some experience at 500 and 1000pts (i'd like to hear more from the folks who were at the Battle of Hoth recreation and the battle of the grassy plains recreation etc).

be prepared for it to be a 4-8hr thing,

in terms of CEs etc,
you can keep it being board wide - your commanders are going to be prime targets immediately for things like Missiles (board wide, no range hehe)
blaster barrage and impulsive shot etc,
those can attack each legal target... so, you could houserule "only 10 targets for those" beforehand, whatever you choose,
make sure everyone knows the rules before the game and be consistent in application hehe
you can also try replacing the map grid with inches instead, and play like SW40K

I found SWRPG mass battle rules and SW40K (a variant of GW40K)
offered a quicker runtime and a little more strategy. for those ultra massive battles.

If you wanted to limit CEs, you could suggest no CE may be more than 12 squares (mouse droids and Mas Amedda count from their position also). Though, most folks'll advocate for boardwide if there's no range limit stated.

Good luck, and hopefully it runs well

@EmporerDragon,
that's a good idea, I may have to borrow it in the next large scale battle

I always thought, SWM should have some kind of "squad rules" for large scale battles, where you move and attack with groups of minis.
I always hoped WotC would come up with something like that for large scale battles after they made the AT-AT, but sadly it never happened.
Which I can not really understand, because it would have made sense from a marketing point of view, to encourage to have a big collection, bigger than you really need for a skirmish game (but maybe they just knew we all would end up with waaay more minis than we can ever field ).