Depending on the utilization (i.e. somewhat low utilization) you could save some money in the cloud if you compare it to the usual 5 years depreciation cycle.
But for scientific computing you usually still use your computing nodes longer than the 5 years of depreciation/support contract (often until they are close to fail).
Another reason why cloud is not very attractive is with how budgeting rules work in those old institutions. You propose a cluster and get the money, all calculated from the start. On-demand cloud pricing will be very hard to get approval for.
> [...] other costs like networking and storage [...] I am currently using the equivalent 20k dollar in yearly EBS costs on our scientific computing cluster. You can buy a lot of storage for that. And the internal IT department that exists anyway will manage it.
Cloud can be a very hard sell to scientist.
Edit (a point I forgot): Cloud only makes sense if you can use spot market capacity extensively, then it can become very competitive with local installations (again depending on required utilization).