They wouldn't have Thrawn, he had already left for the unknown regions and hadn't thought about returning for several years yet.
According to several bits of lore, most recently the novel
Choices of One, Thrawn still participated in galactic affairs during the period between Yavin and Endor. He was responsible for several intelligence operations that helped locate rebel cells and bases, directly participating in at least two of them.
As for units, if its a full scale galactic conquest, it would be a great opportunity to bring back that unit I liked, the Tie Phantom since this would be the time period is was produced in.
Other units, for the empire should be pretty much all of their era one ships but include the tector and praetor II since any combats should be in the outer sectors of the galaxy and those were supposed to be less popular ships which would have been relegated to those sectors. If it was feasible, it might make sense to put a current build limit on tie defenders to reinforce their rarity at this time. The empire could also use skipray blastboats since they enployed those, or if you were feeling ambitious enough to add a new ship to the mod, Xg-1 Star Wing (assault gunboat) were supposed to be standard complement on all imperial star destroyers.
I agree with the idea of not garrisoning A-wings and B-wings except possibly on hero units, and as for capital ships, depending on just how brutally and realistically outgunned the rebels should be, limiting the number of capital ships that they can have at one time might be an idea. Alternatively, I wouldn't mind seeing them get a couple of the other ships they had in star wars rebellion, since someone mentioned the dauntless class.
Heros, Baron Fel, Mara Jade, Hand of judgement, Veers, Piett, Thrawn, Ozzel, heck even Xizor, Vader, Palpatine, would all be good choices, if you wanted to be really mean you could throw in a bunch of the PA heros and warlords who served the empire, though I admit handing the empire several heroes with SSDs right at the start might be a bit rough.
Rebels could have Crix Madine, Luke, Leia, Han+Chewie, Lando, Ackbar, Carlist Rieken, Airen Cracken, Kyle Katarn+ Jan Ors, luke would probably be leading rogue squadron but if not you could put Wedge in, Winter, thats all off the top of my head for Rebel scum, but I am sure there are several more.
Planets, I think it should be mostly planets from the outer rim, mid rim, and wild space with a small amount of the core, and Maybe a tiny amount of the Unknown regions, since between the Battle of Yavin and the Battle of Endor, the Alliance did not if I recall have very much influence in most of the core regions, since most of them were very loyal to the empire and even Palpatine himself. All of the planets featured in the original rogue squadron game would be decent choices, Hoth, Tattooine, Barkesh, Chorax, Corellia Gerrard V Kile II, Kessel (the Maw by extension), Taloraan, Fest, Chandrila, Sullust, and Thyferra.
That's all I can think of right now, will post more if I think of it.
EDIT: If memory serves Just prior to the Battle of Endor wasn't the empire supposed to have around 25,000 Imperial II star destroyers? Not sure I would call that super rare.