As others have mentioned, booking.com makes it easy to communicate with the hotel. I've always gotten a quick response. It's standard for me to message the hotel, saying I need a room with good Wi-Fi reception. Responses indicate that hotels do read those emails, though a prudent hotel will always warn that it cannot guarantee to meet such requests. Depending on what I've read in reviews and the hotel's facilities, I sometimes also request a room on the quiet side of the building and/or one on a lower floor (if there is no elevator).
I don't expect always to get what I've asked for, but it seems to work more often than not, and the reception staff often mention my request when I check in. Mind you, I am not asking for premium features for which one would expect to pay extra, like a balcony or a great view.
As far as I know, booking.com doesn't block-book rooms and re-sell them to travelers; I've seen no sign of that. I suspect hotels.com does that, and I'm nearly certain Expedia does. I think the usual sign of third-party-controlled rooms is a slew of prominently-displayed promotions for non-refundable rooms. In my experience, if you work through booking.com, you will have a refundable option for just about every property, with the possible exception of extremely high-demand periods like Holy Week in Andalucia (or perhaps Oktoberfest in Munich).