I think part of the reason why it bugged me is that here you essentially had a clone who was a Jason Bourne type character, where you could explore the nature of his organization from someone who was both an insider and (now) an outsider, and can touch on themes such as whether the ends justify the means and who are the real good guys and bad guys and so forth, or whether such a distinction really has meaning. Obviously that's kind of heavy stuff for a 22-minute animated kid's show, but it has tackled those issues before with the episodes featuring the Seperatists who had legitimate grievances against the Republic.
Apart from the problem of minimizing slavery when it's done by the people who you are ostensibly supposed to be rooting for, it just felt like a missed opportunity to explore something more meaningful instead of just having Gregor regain his memory and then instantly be all gung ho to go back to being cannon fodder for the Republic again. And it also could coincide with the droid's own treatment by Gascon and others. Many of them are clearly sentient beings who are treated as disposable tools by their masters.
What's the point in doing these multiple-episode arcs if they're not going to get into some more thought provoking or hard-hitting themes? It's just felt like three or four disconnected mini-missions so far except for the involvement of the same core characters (who are mostly annoying).