Working on Rebels is a good idea. At this stage of the game you're not remotely ready for LS Geonosis Territory Battle. Although it's a guild decision, if you're an average or above average player in your guild, you're probably still playing the Hoth Territory Battle. Rebels are required here.
There are also a couple spots on DS Hoth where Empire are required, but there are more that are limited to Imperial Troopers. There are none that require separatists. Obviously you need separatists in the long run, but the clear winner here, I think, is Thrawn.
Of course, you've also expressed an interest in Padme, where Thrown can't help you but Dooku can. You are a good long way away from getting a 7* Padme. Dooku without a zeta isn't very good for Padme's event, but can get by with relatively lower gear and no zeta for unlocking Padme, allowing you to start slowly gearing her up. (To advance there good ideas for characters to work on include Ventress, B-2, Droideka and GeoSpy while continuing to gear up Grievous. However, if you play around with mods, you might actually be able to unlock Padme at 5* right now. It wouldn't be easy, but it might be possible. Geo Spy to 5*/g8 or g9 would be the quickest addition to get Padme unlocked, I think.)
Given TB situation + how far you are from 7* Padme but how close you are to unlocking her without needing to improve Dooku + the fact that Thrawn is going to help more in all things related to ships and GAC and possibly even Arena - at least as I expect you're doing in those game modes right now - I'd do Thrawn first and build up Dooku a little later.
That said, I always tell people that if the best advice for efficiently gaining power and progressing through SWGOH content isn't going to turn out to be fun for you, then ALWAYS go with the fun option. It's a game, and it's always going to be a game. You won't make money off this. Combine that with the fact that (as you know) it requires a long, long time to finish any worthwhile effort in the game, choosing efficient goals that aren't any fun turns SWGOH into an unpaid job instead of the fun hobby it was meant to be.