we absolutely have to have layer control when in the Ortho Cube. as of now (2014 Ext2) if you turn a layer off while in ortho cube it still shows up when creating the new view. you can turn layers on/off here but it is not functional as it leaves a "cut out" or will not reveal an object underneath it.
futhermore you have to go into every single model you are referencing and adjust layer control, cut ortho dwgs, go back to references and restore layers. time consuming and annoying.
the ortho generator has come a long way but this is a major issue for us.
Product enhancement recommendations can be submitted here:
There is actually an existing enhancement request logged for this with our Plant Development Team. They will be looking to see if this can be addressed in a future fix or upcoming release.
In addition to the feedback link above, please leave your feedback on the Autodesk Plant Exchange Feedback site as well. This is a direct place to send you ideals to let the Plant team know what improvements you would like to see.