Dominik,
I'll be sure to let you know how we go with UCS. Our deployment is strictly for a large-ish VDI rollout at this stage, but may expand to a more general compute solution later. Coming from HP's C-series enclosures, and some of their nasty interconnect solutions, i'm very keen to see how a real network company does blade networking. From the training i've had it seems reasonable, but the proof is in the prod!
As for the 5ks: It seems that FlexPod includes them in order to allow vPC connections to the NetApp filers and the Nexus 1000v appliances, and to provide more fibre channel ports for disk. The Fabric Interconnects will work in 2 modes, 'End Host Mode' and 'switch' mode, neither of them provide that much layer 2 switch functionality, and no layer 3 at all. It seems you need the 5ks if you want to do anything too tricky.
You're right though, i believe that the 6120s are the same hardware as the 5500s, but running different code. We're actually getting the newer Fabric Interconnects, the 6200s, but i'm not sure what the difference is, apart from more ports and the 2.0 software.