If you go down the Passthrough route, you will loose all new functionality when it’s released through the GRID software updates. By not using vGPU (GRID), you effectively go down a hardware only route, where there is no feature development as it’s all built into the GRID software. Sure, you have a Windows GPU driver, but that’s it.
Regarding not using vMotion for XenApp, how do you apply updates to your ESX hosts? Would it not be beneficial to be able to migrate your VMs to another ESX host without having to drain and power down your XenApp VMs to restart the host?
I wouldn’t base your decision on the current GRID 4.3 release, make sure you evaluate the GRID 5 release coming on September 1st. There’s a lot of new features in this release that may make it worth while :-)