What I don't understand is why anyone would want to buy one of these things. I've owned Nexus devices, Touchwiz devices, and Sense devices. Every one of them at some point or another has been flashed to stock. I personally prefer the look and feel of stock Android, so let's not knock me for that.
The thing with some of these ideas the OEMs are packaging into their custom Android versions is I don't want to do without them. I've run into this twice. Once with my Note 2: S-Pen functionality that you didn't get flashing Cyanogen. Now with my HTC One: the cool camera stuff, Beats, (and maybe Blinkfeed, I'm still on the fence) You know those speakers won't perform as well without Beats.
Buying the device from the carrier, however, means I get to make a choice. I can choose to use, or not use the features included in Sense (or Touchwiz). I can choose to use, or not use stock Android. I have more choice buying a carrier device (or direct from HTC).
There are always guys out there (thanks to them btw) creating really great experiences in the form of roms. If I want stock Android, there are going to be plenty of Senseless roms out there (Cyanogen, notably). If I want Sense, but with different menus, I can probably find a rom for that. The springy thing the menus do is sort of strange, and I don't care for it. I can find a rom without that.
Now all this said, I'm not a rom chef. I'm not much of a developer of any sort. If it'll be possible, after buying one of these "Google Edition" or whatever they're going to call them phones to throw a Sense rom on there great. If not, you should probably think about whether or not you would like the option to have it. Hell, I could be totally wrong and they could make it vanilla Android with Beats and Zoes/Highlights. I've been wrong before, and I'll be wrong again. I don't think it'd be surprising to see it. If we don't see it, though, think about some of these things before you spend a lot of money on a phone. I wouldn't want to be sorry about missing out on some great features and experiences.