Those are some very good points that you brought up and ones we are taking into account with our model. There are certainly disadvantages in using a cloud especially with the network being a bottleneck and the overhead of maintaining the virtualized infrastructure (via Open Nebula, etc.) However, with specialized supercomputers you have the big problem of scalability, even though it offers higher throughput there is a drawback to how many CPU's, processes, etc. that are available. If the supercomputer is simply for your own use, then yes, there would be no justification for a cloud. However, if you consider various applications such as Blast, GROMACS, MM5 which can (and are) used by a big sector of the scientific community then scalability and availability are big problems. Supercomputers have long waiting lists and you often cannot use its entire computing power. This is another reason why I wanted to get into Cloud b/c there are a lot of challenging problems (scheduling, networking, load-balancing, federation). I'm curious, what are your research interests in HPC?
What I said, on second thought, might be a little confusing since I talk about supercomputers and not grids. Maybe it would be more accurate to say that the research I'm doing is geared towards seeing if HPC applications are affected by virtualization technologies, some grids do leverage virtualization which is why I did not want to generalize.
Thanks, newms! You're right about the research, I really should target schools known for their presence in Cloud and HPC since I know what I'm really interested in.