Q. Are their limitations on changing the SKU of a VM with Azure Resource Manager?
A. Not really. There were various restrictions with Azure Service Manager (ASM) and changing SKUs however with Azure Resource Manager (ARM) there are no such restrictions. Simply shutdown the VM, change the VM SKU then restart. The only limitation on changing the SKU would be if using premium storage for the VM which would block changing the VM to a non
<something>S series VM.
Additionally if VMs are in an Availiability Set (which exists in a single stamp) then the possible SKUs will be limited to those supported by the stamp.