A couple of you have hit on this, and I want to hit on some of your points.
Some of you haven't seen E1, for whatever reason. I don't think that makes you bad fans. Quite the contrary.
I'm one who isn't incredibly impressed with E1. Don't get me wrong--I like it. But I wasn't blown away by it. The reason being is that there was no context. Suddenly, we're 10 years in the future, with no reason to be 10 years into the future. "Oh, look at the flashbacks... apparently, the apocalypse started due to real people being remotely wiped? OK..."
Joss didn't write either episode. Maurissa Tancharoen and Jed Whedon did. Yes, Joss approved it, but neither E1 nor E2 were Joss'.
So, they are basing a finale around an unaired episode. Not only that, E1 was never meant to air. It was an experiment to see if they could shoot an episode on cheaper video tape whil they were filming "Omega." E1 was only meant for the DVD, a 13th episode in order to have the season 1 DVD come out.
Now, some people couldn't afford season 1 on DVD, so they haven't bought it or watched E1. That doesn't make them fail as fans. Others have the DVD, but chose not to watch E1, because, given an idea world, Dollhouse would have built to E1 and they didn't want to spoil themselves.
Maybe, once we saw that the finale was going to be based off E1, they could have found E1 somewhere. But, they didn't. That was their decision.
I personally think it's ridiculous to base a series finale off an unaired episode. But, just because you haven't seen E1 doesn't make you fail as fans. So, the ones of us who have seen E1 and knew a little of what was going on shouldn't be implying that either.
E1 is all over the internet. It's not as if it is necessary to buy the DVD's to see it.