This can be solved by moving overall focus from "planet management" toward "system management" with planets being only a part of it, in almost every aspect (POP distribution included).I would like to see a more Astromineing heavy focused mineral production. But my fear is that wide Empires get to much advantage out of this. I hope they manage to balance it with the new Trading and Resource mechanics.
In conclusion the most important thing in a game is balancing. So if it isn't possible to make it play mechanically feasible with the current playable Empire types I can understand if they choose to implement the hole thing differently.
"Tall vs. wide" can be solved with something similar to EU province development, so you can heavily invest in overall "development level" of a system. You either grab system around and focus on "best spots" or consistently improve a handful of system. Maybe you can even do something like "meticulous surveying" to uncover new resources\anomalies in already explored systems if they are developed enough.