I finally installed Windows 8.1 on my 13" 2013 retina MacBook Pro, but it took some doing and a little help from other posts.
Ultimately, what worked was an ISO install via EFI Boot.
I used Boot Camp Assistant to install a Win 8.1 ISO to a USB flash drive along with Apple's driver setup (first two checkboxes).
Boot Camp Assistant will rename the drive WININSTALL.
During the process you may be prompted for your Mac OS username and password to allow the process to continue. If it fails, you probably left it alone too long like I did the first time.
Because my original copy of Windows 8 came on disk, I had to use the following technique to download an ISO: http://www.neowin.net/news/here-is-how-to-get-the-windows-81-iso-and-create-a-us b-install-stick
Unfortunately, when I first attempted to install Windows using the ISO downloaded using the above process, Windows setup would not accept my license key. Unlike Windows 7, there wasn't an option to leave the key blank and activate Windows later.
After a little more research, I found the following article about a Microsoft-supported process to restore that option: http://www.jmedved.com/2013/09/installing-windows-8-1-or-8-without-a-product-key /
I also found the ei.cfg mentioned in the comments here (Robin Tick's post):
http://winsupersite.com/windows-8/windows-81-tip-download-windows-81-iso-windows -8-product-key
The process involves adding an ei.cfg file to the sources folder on the WININSTALL thumb drive created by the Boot Camp Assistant..
The body of the ei.cfg file should contain the following (well, this worked for me and was recommended by other posts):
[EditionID]
Professional
[Channel]
Retail
[VL]
0
However, in order to ensure the ei.cfg file will be read properly by the setup process, I would create the .cfg file with Notepad in Windows (hopefully, you have another Windows machine around).
First save the file as ei.txt then rename it ei.cfg. Click OK to the usual warning prompt about changing Windows file extentions. Finally, transfer the ei.cfg file you've created to the sources folder on the WININSTALL USB drive.
Phew!
Yeah, that's a lot of hoops and tedium. If you have a Microsoft volume license and are able to download a traditional ISO, you shouldn't experience the same trouble I did.
Anyway, once the WININSTALL USB drive was prepared (with efi.cfg file in the sources folder), I plugged it back into Mac, restarted, held the option key, selected EFI boot and let her go. I did try selecting Wininstall as the boot device, but that lead to a GPT error (you can't install windows on this partition... yada yada yada).
This time I was actually able to enter my license key at the appropriate point. I had thought I'd have to leave it blank and enter it via activation the System control panel.
This technique seems to ensure Apple's keyboard drivers are installed before the customization screen (so you'll be able to use the keyboard and trackpad). It also runs the full Windows Boot Camp driver/utility suite prior to completion so there's very little to do once Windows boots.
I hope this helps. Enjoy!