Well you've made up my mind!
The official Rebel Alliance of the movies may have only gained official recognition via that timeline but if I ever get a game up and running I'm planning on having it start from the tail end of the Clone Wars and for some the Separatist conflict didn't end they just had to recognise the true enemy.
I always assumed Bail Organa began the Rebel movement following what he witnessed at the Jedi Temple, the information Yoda would have revealed about who Darth Sidious really was as well as the true ramification once Obi-Wan joined them made it very unlikely he would have just toed the line and not done anything about it.
I never got very far with the Dawn of Defiance game they released and now wished I'd kept a copy to review since I assumed that was how the Rebel Alliance got up and running with Bail organising things with Mon Mothma and the other guy until those two quarrelled over trying to separate military and political matters since one was better at one and lousy at the other.
I never thought much about Force Unleashed save for the cloning side which I thought showed an interesting idea, I can't see the Empire allowing any planetary defence forces to remain outside of their control unless they're more ceremonial like Naboo's fighter unit was considered.
One thing I hope Rebels show is how the Empire deals with establishing new bases, only problem I can think of is how do they secure things so that even 15 years later the general public are still in the dark about the Empire's activities?
I keep wondering if Compnor helps by organising events to promote the Empire and also establishing the very rebels to act as the scapegoat for their activities that they don't want linked to them...