From a capability standpoint, Hyper-V Server R2 is essentially the same as the Hyper-V role on a Windows Server 2008 R2 installation.
From a "technical limitations" standpoint, going with Hyper-V server is actually better than going with Windows Server 2008 R2 Standard. Hyper-V Server R2 supports up to 1TB of memory and 8 (multi-core) CPUs. Windows Server 2008 Standard supports up to 32GB of memory and 4 (multi-core) CPUs.
If you compare memory/CPUs to Windows Server 2008 Enterprise or Datacenter, then Hyper-V starts to fall a little short. Enterprise supports 2TB memory and 8 CPUs, Datacenter supports 2TB and 64 CPUs.
I know you said to ignore licensing - but the other big factor is the included free guest licenses on Windows 2008 Server. Hyper-V Server includes none. Standard includes 1 free guest OS license, Enterprise includes 4, and Datacenter allows unlimited. You need to do the comparison between purchasing guest OS licenses or purchasing the "upgraded" host OS and using the included licenses.