Except vDR is no longer a supported product, so we'd be talking about VDP.
Not true. VDR is still fully supported, but yes, it is true that it is not developed anymore. Anyway, version 2.0.1 is very stable and has everything that we need.
VDP has HARD limits, there's no way around the sizing issues.
Unfortunately, VDP has many other limits and lacks some functionality that are present in VDR, but not in VDP. That's the main reason we are still on VDR. Hopefully the next version(s) of VDP will catch-up with VDR and then we'll switch to VDP. So I have still no experience with VDP by now.
but even systems small VMs seemed to run backups for entire nights
Then something is wrong in your environment configuration. What kind of storage are you using and how it is connected (FC, iSCSI) for the VMs and for the VDR destinations? Make sure that VDR never backups the VMs to the storage where VMs lives (which would be a nonsense, anyway).