Fusion does not allow the user to send a power off or restart command to virtual hardware when connected to an ESXi host or vCenter. So if a VM crashes, halts or otherwise needs a hard power off or reboot, the user has to log into vCenter or use the ESXi thin client.
Uploading OS X VM's to supported ESXi 6 hosts, such as a Mac Mini or Pro, does not work. They usually won't upload, and if you do get them there manually, they won't run.
Fusion forces the user to use Hardware level 12 for 10.11 VM's, but that makes it impossible to deploy 10.11 onto an ESXi host. Since 10.11 is almost impossible to install directly on an ESXi host by pushing up an ISO, this basically means building a 10.9 VM and then upgrading it to 10.11 after it is running on ESXi. Of course 10.11 runs just fine on hardware version 11, so this is an extremely tedious and time consuming workaround.
Snapshots taken of a VM on an ESXi host from within Fusion may become invisible to Fusion.
All function keys must be selectable in the drop down given the default mapping of the keys on OS X and the fact that on desktop keyboards, Apple does not give you a hard Fn key. Fusion cannot be limited to just offering the high function keys (for example, sending F2 to a vCenter Server Appliance is flaky without this).
Creating a new OS X VM on an ESXi host from within Fusion should allow choosing the Install OS X App as a local install disk the same way as it does when creating a new local OS X Vm in Fusion. Since this already works for local installs of OS X, this would massively improve the experience of building and deploying a clean OS X VM onto ESXi.
Apple-branded USB-Ethernet adapters cannot be set as attached at power on for Fusion VM's. This means that VM's that should have a separate physical interface must have their settings menu opened every time they are power cycled. It is not feasible to select from the bar across the top because if there is more than one connected to the system they are all named "Apple USB Ethernet..." so the user has no way of knowing which is the correct one.
Fusion needs a nanny-free mode. I find it extremely annoying to be constantly asked if I want to do the thing I just instructed it to do. It's like using Windows 98 again. "Are you sure you want to shut down your guest?" "Yes damnit! I didn't choose it by accident and if I did then let me pay the price and just do it already!"