Yes you could do that.
Build a brand new vCenter.
Migrate all the machines and free up a host from old vCenter. Upgrade/install ESXi on the vCenter. Add it to the new one.
Disconnect+remove the other hosts from old vCenter and add them to new one. Move the VM's to new ESXi and bring down those hosts and install/upgrade Esxi 5.5 each at a time.
Then create required clusters and add the hosts
Also consolidate the servers like you have planned.
Also consider the pints i mentioned about creating a new cluster.
Be sure of all the best practices and follow all the required guides.