I'm having the same problem running El Capitan 10.11.1 and VMware Fusion 6.0.6 on a MacBook Pro (Retina, 15-inch, Mid 2014).
I also have hibernatemode set to 25 and destroyfvkeyonstandby to 1 and when waking laptop after hibernate I'm able to enter the File Vault password but then the trackpad and keyboard freezes on User login.
However, I don't need to restart the laptop to regain control. If I instead close the lid one more time when I'm at the frozen User login (after entering File Vault password) and leave it for 2 - 5 minutes (haven't checked how long it takes..) and then open the lid again, then Voila! and I can enter my login password and everything works like it should, even if the Virtual machine is running. Hope this can be of help to someone...
Another issue I'm having, which I don't think is related to the freeze issue, is that if I connect/disconnect the power when I'm in sleep/hibernate then the computer crashes/shuts down instantly. So I'm forced to do a little ritual every time I disconnect the power and move with my laptop to avoid the unnecessary shut down/crash... Very annoying.
If I suspend/quit VMware before sleep/hibernate then the machine will wake without problems, so it definitely has something to do with VMware Fusion.