I'd try to steer away from peoples "gut feel" for performance and get numbers to do the talking.
I use a variety of benchmarking tools to evaluate the performance. Since it's about user experience you need to consider the type of user, Task, Knowledge, Power user etc.
I can't address what is the "best" protocol as it's really a moving target and has many factors, but our baselines are in a XenDesktop environment with ESX etc. We have images with SAS storage and EFDs for cache drives.
Now the Q is: How can I evaluate and compare the effectiveness of
remote desktop protocols based on the quality of their user
experience?
Tools I use are..
OSMark
It's a great tool I customise the tests to suit the environment eg. CPU intensive, Graphic and so on. I can then compare rendering of RichText, Web and 3D objects when I make changes to the environment and relate back to the baseline. Youcan also run the same tests on a physical machine to look at the variance.
Crystal Mark
Benchmark disk performance, good for "Internal to VDI" testing of a VDI disk\network performance.
If you have a Citrix Environment, EdgeSight for Load Testing is great as well.
While this does not address your problem in particular it might help determine your bottlenecks and create load on the system for other testing.
You may need to look into QOS for your telephony stream and seperate the traffic once your determine what is most important. Look at if you can change compression in your telephony system as well.
Hope this helps, or is useful to anyone passing through.
jezr