Okay, so the one thing folks don't seem to be mentioning in their reviews is the little girl. Susan.
In order for Topher to have an imprint of young Susan's brain to mature it into older Susan with good influences, they must, at some point, have nabbed little Susan and gotten her into the Dollhouse in order to get that imprint. She has been in the chair. People seem to have missed the whole discussion wherein Topher explains that he has talked DeWitt into allowing/funding the experiment, meaning no outside source paid for Echo to be there; the orphanage(?) just happened to be a handy source of research subjects.
Being the sick minded creature I am, my thoughts went back to the fetuses that Caroline and her friend saw in the lab when they broke in. What if all the kids at that orphanage are actually products of the Dollhouse's other research initiatives? What better way to see how your brain arranging software works than to test it on dysfunctional kids you've already created.
So many fans are acting as if it's a big scary shock that the lovely doc played by Amy Acker might be a doll. Hello, am I the only one who thinks perhaps the handlers and DeWitt are the only non-dolls in the place? Topher and the doc both seem very educated and experienced for their age. Usually the kind of competitive nature Topher has shown about scientific research only develops with age and lots of previously lost competitions. Why would the Dollhouse risk exposure and spend money for salaries when they can just tweak actives with the personalities and skills they need? Why not have a few brilliant but reclusive people whose personalities you can recycle?
There are more than twenty Dollhouses according to what Echo told Ballard -- what if you walked into any one of those and found a Topher and a Dr. Saunders, maybe an Ivy as well.
I think a number of viewers either aren't used to the way Joss thinks, or they just aren't suspicious/paranoid enough in general.