Surprisingly, yes - from an interview with Tim Minear:
AX: Was there any discussion on DOLLHOUSE about what Season Three might be, or did everybody think, “There is no way in hell this is going beyond Season Two”?
MINEAR: Well, it’s funny, because there wasn’t a huge talk about Season Two [laughs], because we thought there was no way in hell it was going beyond Season One, which is why we did that episode that didn’t even air, “Epitaph One,” or as it was known at the time, “Epitaph” [laughs]. We thought that was going to be the end of the show. And so when we came back to do Season Two, “Epitaph One” ended up being the bane of my existence. I wrote and directed my last episode, which actually had a scene from “Epitaph One,” but I had to try and make sense of everything that had gone on in Season Two in order to get us to this big reveal of Boyd at the end of that episode. I also had to keep in mind “Epitaph One,” even though it hadn’t aired. What I didn’t want to do, for people who watched it on DVD later, was for them to say, “Well, that doesn’t match to what they said happens later in ‘Epitaph One.’” So it was a giant puzzle. So no, there wasn’t a lot of talk after Season One, but your question is, was there talk at the end of Season Two? Because of the fact that we had this extraordinary second season happen, which no one was expecting, we actually did start talking about Season Three [laughs]. Which just goes to show you.
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AX: What would have happened in DOLLHOUSE Season Three?
MINEAR: Well, I think one thing that helped Season Two was that we got canceled, because remember, we got canceled before we finished that run, so we had to take the last four or five episodes and cram a lot of what would have been in Season Three into Season Two, and what that ended up doing was, it gave it a certain amount of momentum in the second half of Season Two that I’m not sure it would have had had we not had the axe dropped on us prematurely, or maybe it wasn’t prematurely – it’s hard to say.
What I think we came to was, by having Echo become this sort of superhero and having her become the sum of all these different imprints, of all these parts, and allow her to become this sentient being with [all of this incorporated into her], we found a way to make her a character. I think the problem in Season One was, you had this concept that sounds great when you’re pitching it, but when you sit down to write it, it’s, “Okay, so now we’re writing a show about a main character who can’t remember what happened last week.” Which I think was a little boring for the audience, because they’re so far ahead of her. So when we started allowing her to remember things, and then started taking the concept and making it into what her superpower was, it started turning into something else. I think what you would have seen in Season Three is [a series] a lot more embracing of its mythology and turned into more of a superhero show. It would have been a little bit more like BUFFY in some ways.