I didn't finish Makeb story yet, so I'm not going to read through this thread to avoid big spoilers, but from what I know, I think it's real shame how devs treat us. Already in vanilla, I wasn't convinced by the way they explained loss of Corellia after I basically drove the Republic of the planet in Darth Decimus storyline. All this feels like it doesn't really matter what u do. They will decide what happens next and be sure it's not going to be good for Empire.
If you did every single world arc, from Dromund Kaas to Corellia, it's not really that hard to understand how the Republic was able to drive the Empire out; Just take into consideration this...
On Hoth, you have a retired high ranking officer, who's willing to sacrifice thousands(!!!) of soldiers to reach a stalemate with the Republic, despite not being able to proove it's actually worth the bother.
On Dromund Kaas, you have a Sith Lord who prefers to waste his time - and that of the imperial military - on a pointless slave rebellion, that should be put to rest swiftly and efficiently and instead, the latter decides to prolong it. On the same planet, the cradle of the imperial might, you have Sith infighting that further weakens the order and the military, since the former answers to the latter.
On Corellia alone, according to Darth Malgus, the Empire lost a tenth(!!!) of its forces, during the time of the occupation and before they were driven out of the planet, not to mention that the Empire is not capable, for the most part, of working with the locals, without stabbing them in the back eventually.
Having all this in mind, you seriously fail to understand how the Republic was able to drive them out? I could go on but i'm trying not to go into spoiler land.