Well, maybe I posted to the wrong forum...
I went in to speak with a mac genius too. All I got was, "In all the years I've worked on Macs, I've never seen the migration assistant with greyed out options." Ok. I guess I have more experience, I've seen it. They then suggested I run check permissions on the drive and buy Disk Warrior for $100. Sorry guys, the drive is fine. My TM backups are fine. It's not that.
I went ahead and bought a 1 TB drive. Even then, the migration assistant choices were greyed out. I went ahead and created a Fusion drive to take advantage of the SSD (the 1TB is only 5400 RPM). The directions can be found here. I then just ignored the greyed out options and brought *all* the data over to the 1.1TB drive. Everything works fine.
I'm bummed about not getting the apps and O/S pinned to the SSD but I figure if anything is getting used a lot, its where it needs to be.
Just wanted to chime in, I guess we're the only two people in the world who have experienced this problem. I was upgrading an XServe from 10.6.8 server to 10.8.4 and wanted to only migrate settings and configuration. No dice, all checkboxes in the Setup Assistant and the Migration Assistant were grayed out.
I tried multiple iterations, installing from a USB clone (instead of an internal drive), creating a new user - nothing made any difference. I ended up skipping this procedure altogether and manually migrated what I needed.
I was trying to migrate from a local disk that had the old OS.