This is an update to previous posts of mine in this same thread. Like others have done, I too had Apple replace my 13" rMBP 2.4/256/16GB system with a brand new one.
I picked it up today and the issue persists. The EFI update came preinstalled as I am running the latest boot room (MBP111.0138.B03). I also have ensured all updates are installed.
Note: The system works "fine" (keyboard and trackpad operate) on a clean install but will not allow the keyboard / trackpad to function as desired after I use migration assistant. I have also tried to boot from known good external drives and the system will not mount the root device. I have tried these same 10.9.1 OS external hard drives with Late 2011, Late 2012 and Mid 2013 systems and all of them will boot up fine. It is only the late 2013 rMBP with Haswell that seems to be an issue.
I checked my console log and this is the same error that other users are seeing and I am seeing ON A CLEAN INSTALL as well. I see this error listed SEVERAL times.
1/3/14 10:32:04.000 PM kernel[0]: The USB device Apple Internal Keyboard / Trackpad (Port 5 of Hub at 0x14000000) may have caused a wake by issuing a remote wakeup (2)
I can get it to work, kind of, by jerry rigging it but it is not a full proof solution. I had to create a new profile, on a new install and import data, which is cumbersome to say the least. Again, my hard drives (current and fully up-to-date OS X 10.9.1) and time machine backups work on EVERY OTHER SYSTEM except the 13" Late 2013 rMBP.
At this point, I'm not sure if it is best to wipe the system and return it seeing as Apple clearly doesn't want to accept responsibility of this catastrophic failure and properly address it to offer a fix or if I should allow the Apple rep I am working with to contact his engineers as previously discussed. I would hate to keep the system and discover that a fix will never be released which results in an expensive paperweight. I fully expect this to be a result of both hardware and software and the way the software addresses said hardware considering the system works outside of 10.9.1 Mavericks.