"It's the repeat of St Vincent that has got me thinking that they couldn't find any female alternatives, so went with someone who has already recently played twice in order to keep the quotas up." Let's think about that...
I do personally find the repeat booking of St Vincent a little uninspired, although she was one of the most popular acts of the weekend, so clearly not a problem for most.
I don't think it has anything to do with gender, though. I can't say there's much quota-filling or positive discrimination going on... Take last year's headliners, for example, where we had two all-male bands and a solo male. The year prior featured a favourite of many EOTR-goers (Joanna Newsom) and then two arguably quite weak headliners (Bat For Lashes and Animal Collective) although, again, I don't think Newsom nor BfL were booked for their gender (in fact I know Newsom was demanded by a lot of fans AND I spoke to Simon the year before she played and he told me he was hoping to book her...). The year before that was two all-male bands and a solo male... & so on.
Point is, complaints of quota-filling are unfounded. We're in a moment that is rich with female-fronted indie music, and in which there are conscious moves to open the field up to those that aren't men. As such, there's an abundance of popular female artists at the moment but, perhaps, few are of "headline" size yet.
I really enjoyed Feist and thought St V was ok, too. Beyond them, there's a number of female acts that will be vying for headline / high spots in the coming years: Courtney Barnett, Angel Olsen, Sharon Van Etten, Waxahatchee, Jenny Lewis and so on... Then there's Snail Mail, Haley Heynderickx, Julie Byrne, Torres, Soccer Mommy, Big Thief who've played in recent years and will continue to grow in reputation... And then, of course, heavyweights like Bjork and Fiona Apple and PJ Harvey who are arguably too big for the festival.