So I'm curious. Do you regret this decision? I've been toying with this idea but I keep thinking that managing data for two machines is too much work. I currently have a thunderbolt display + 17" mbp but I'm upgrading next revision.
No, I do not. The main motivation for doing this was that the 27 imac essentially offers the same (more!) value as the Thunderbolt Display. The fact that you can use the 27 imac as a secondary display for the rMBP means that nothing would change really (except from gaining a second computer). It works just as flawless when using a simple (cheap) mdp to mdp cable as it would with the Thunderbolt Display. So I still often use this combo and its not really different.
As for file managing. I have all my documents stored in Dropbox and films on my home server. I listen to music via spotify. So, to be honest, I don't have any problems since I can access it all from both Macs. I don't have much more stored on my Mac(s). Simple.
I have the same iPhoto library on both Macs with fotostream enabled. I actually gained 1TB of storage for files (that I don't really use).
So, in a nutshell, no regrets at all.