I applaud your suggestions for an update of the primitive interface, but the current functionality is not bad for a free motion graphics editor.
Once you've created a multi-composition project, as described above, you can see multiple compositions (by name, rather than thumbnail) and quickly modify composition order, in both layer order and time order. It is nowhere near as pretty as thumbnails, but it works (especially if you give your compositions meaningful names).
What's more, you can animate compositions on the canvas and timeline, giving you movement within movement.