I quickly found out that Migration Assistant in Mavericks over Thunderbolt is mostly broken.
Not a problem for me, I know how to use rsync with --exclude!
After getting my user directories moved over I found something rather annoying. MAS still showed that I had installed a bunch of updates, particularly developer seeds, that I most certainly was not running on this new machine.
I poked around for a few minutes with pkgutil, ls'd a bunch of folders, poked & prodded until finally throwing my hands up in exasperation.
Where the heck is this coming from!?!
I methodically started going through my User-level Library (as I now knew the updates only showed up for my standard user and not the admin) and found the offender.
After banishing this annoying little bugger to to the Trash my update list is free and clear.