Gotcha...I'm a NetApp Employee (CSE) so I don't have any VMs of my own but do have clients running 2012. I'm just not sure of the disk type. The Disk type should not however matter as long as it can keep up with the IO demands on it. I would be surprised if a single 2012 server not running anything was maxing out a SATA Aggr. If it did, everything on the aggr should be slow which you did not indicate was the case.
I'm not sure where to start with this though. VMware tools?
Do you know the average latency the 2 different Aggrs are providing?
We had similar issues in our environment running all 15k SAS shelves. We had to make a few tweaks that helped a little but not a lot thus far. Some things I found were the vmxnet3 adapter performs horribly on server 2012 still; We are 100% patched up to the latest 5.1 code and still saw a minor difference going to E1000E adapters. Another fix we found to help with display sluggishness was with the WDDM driver. This was supposed to be fixed in 5.1 and it is to an extent but not fully functional. Check out http://ryanmangansitblog.wordpress.com/2012/09/17/vmware-fix-for-server-2012-virtual-machines-running-on-esxi-5-0/ . I know this is reference to 5.0u1 but it still applied to an extent for us.
That's all we have found thus far. From what I can tell running performance stats the NetApp on the back-end is not the limiter it still seems to be VMware getting the code base optimized. Sorry I couldn't be of more help but rest assured you aren't the only one with issues in a VMware/NetApp/2012 environment.