Moving this discussion to the Installing and activating Flash Builder forum.
I am having same issue.
Have followed the instruction at: http://helpx.adobe.com/flash-builder/kb/overlay-air-sdk-flash-builder.html
When go to compile my mobile flex app I get cant resolve ViewNavigationApplication and new flex mobile projects do not 'finish' when using the wizard.
Have AIRSDK 3.5 with ASC 2.0 is working nicely. Also must remember, when updating SDK need to make sure there are not firewall restrictions to the new commands (adt)
This has solved my ios deployment issue with AIR 3.4 (which was only reason invesigating AIR 3.6 in the first place)
What did you do to get ViewNavigatorApplication and other flex tags to work with the new AIR sdk?
So if you have a Flex mobile application you can't use the ASC 2.0 version of the SDK. On the air sdk download page is a small link that takes you to the right sdk.