PageMaker is to InDesign as After Effects is to...?
Sometimes it is important to start over from the ground up and completely rethink your solution to a problem. I believe it is time for Adobe to do this with AE. Rather than continue to add patchworks of features and solutions here and there, give us a new paradigm in compositing that lives along side AE while this new app is being developed much like you did with InDesign and PageMaker.
Things I'd like to see in this new app are:
A complete reworking of 3D, rather than treating the 3D workspace and objects in it as 2.5d, the successor to AE should be full on 3D with the ability to import many formats like FBX, Alembic, OBJ, etc.
A layer/Node based hybrid workflow. Just look at the node based workflow in C4D or Maya, you can create materials in a node free way but in the back ground the node graph is being built. The successor to Ae should do this as well. Allowing users who are used to the layer based workflow to work as they have always done and then jump into the node editor and see where they can make things more efficient by using one image to drive several elements, etc.
Full 32bit workflow that is Fast, Fast, Fast. Better support for EXR format and workflows.
The ability to play video (with no effects applied) back in REAL-TIME!! NO RENDERING or CACHING!
A procedural animation system for motion graphics that allows, clones, instances, effectors, deformers, etc.
A built-in node based full 3D particle system.
3D text, with real bevel / profile control
That's all I can think of for now, but I imagine that's plenty :-)