I'm using After Effects CC, on El Capitan and would like After Effects to be Full Screen without the dock showing, but still keep the dock from being hidden on the desktop...much like every other program that goes full screen. Right now it stops at the dock and so I'm losing that screen real estate. There is an option under View to Enter Full Screen, but it's grayed out. Any suggestions on how to achieve true full screen mode would be appreciated.
Try turning auto hide on for the dock.
You have an unrealistic expectation that Adobe apps are modern and familiar with OS X.
By modern I mean considerate of the conventions of the user.
By familiar with OS X I mean the last releases.
Step back in time. This is Adobe software.
Rick's answer is correct. So it's: System Preferences > Dock > check Automatically hide and show dock. By clicking on the green plus button in the upper left corner of AE, your screen real estate will be filled to, almost, the max. Almost because I can still see a tiny bit of El Capitan's beautiful green grass. But hey, it's an improvement, right?