Thank you for this. You've managed to articulate something that has been bugging me in not just Whedon's work but many other male writers writing about women, as well. Notably Heroes, Caprica, and Whedon's Dollhouse,
Angel, Doctor Horrible and Firefly, but to a lesser extent Buffy. The comics are only worth addressing here - because they made me aware of the problem.

Which is basically...that we have someone who is writing from a position of privilege, who has not or does not know what it is like to walk across the street and be heckled by construction workers. It's to put it in a broader context - the difficulty many people online have cited about whites writing about persons of color...you will no matter what you do end up projecting your own experience on to it, which I think can be problematic.

Whedon tells the "girl's" empowerment tale from a "male" perspective. His examination of "female romantic tropes" is also from a decisively male outlook. While he should be applauded for attempting to rise above that..I'm not quite sure it is possible in our society to do so - it is so ingrained.
And in the entertainment biz, in particular, the power is with White men. They choose the stories we see, they choose who writes them, who directs, and who produces. A perfect example is Wonder Woman - when that was pitched as an idea - male writers and male directors were the first choices. The comic itself was originally written and drawn by men. It's a woman's tale - but told through a male lense. Mad Men brilliantly critiques this through Penny's debates with her boss Don Draper, when she attempts to say that if it is a female product, shouldn't the female voice be heard - and Don shrugs her off, more or less stating it doesn't matter. An Echo of Roger's similar statement regarding fur coats to Don, it's not the woman who chooses the fur, it's her lover.

Whedon, I believe, much like the writers of Mad Men, is attempting to critique that societal view - in all his art. The difficulty or brick wall he's run into...is well, he can't help but further some of the very stereotypes and negative views that he is attempting to critique. Example - River in Firefly.
A powerful character. But her power is the result of torture and manipulation at male hands. She's been mentally raped and enhanced. It is "her brother" that saves her, not herself.
And finally Mal who saves her and provides her with a purpose.
She becomes in a sense Mal's surrogate daughter. A similar situation occurs - albeit tragically with Fred - who Angel/Wes/Gun and Lorne save from Pylea. She becomes in turns their lover, sister, daughter, girlfriend...and then is betrayed by a male friend/colleague who gives her to an ancient goddess as a new shell/sacrifice. Going back to Buffy ...we get somewhat the same pattern, but as Elsie states, Buffy does manage to save herself, unlike River or Fred.

Moving to Dollhouse - Caroline is a tough woman, strong, saving animals, tries to save her boyfriend, fails, and becomes a sort of vigilante. She is captured by the male run organization she's trying to take down. That organization in turn - wipes her memory and turns her into Echo, does to Caroline what in effect was done to River (and the First Slayer). Echo becomes even more special, even more powerful than Caroline ever was.
And she eventually does take down the male/father, but she also incorporates her male lover into her psyche, he resides inside her head as a sort of separate persona, a conscience - much like Mal becomes River's conscience.

This feels patronizing to me and somewhat creepy. The fact that Whedon sees Dollhouse and Echo's journey in Dollhouse as a triumphant one, a pure journey from helplessness to power, bothers me a bit. And I think the reason it does not work is in part what you articulated above, it's also the reason that the themes in the comics aren't working for me.

Buffy doesn’t begin physically or mentally helpless but she’s still always a girl in a box, whether it’s a box of a destiny she can’t fight (S1) or a box made for one and one alone (S7). Every season, even pretty well every individual fight she gets into, she gets beaten right down but never broken. The story is how she escapes but escape always puts her, Russian Doll style in a new kind of box. S8 is no different. Her apparent power, her fame is yet another box she has to find her way out of.

This is quite brilliant. I love the image of Buffy's journey as constantly escaping the next box Russian Doll style.

Life never gets easier. That's why the hardest thing in this world is to live in it.