Annoying
I am not bothered having an applications folder in my home since I can add other apps I don't want in my main apps folder to it but, seriously, two is completely unacceptable. And no I won't stop sharing because that means I can't use coherence crystal mode which is required on retina MBP for it to show up correctly. I had no problems with this in the beta yet this was added to the release without testing.
Fix this so users don't have to manually hide the folder.
For the users, you can go to terminal and hide the folder using the command "chflags hidden"
chflags hidden drag the folder to hide here
and then press enter.
This will hide it from automatically showing in the dock as well unfortunately so you may want to drag it to the dock first if you like it there, I don't since it has a million apps I will never use. I just drag the app I use instead, if you do that parallels will open and start the app.
This works with any folder so you can hide both if you like.