What are the left over Clusters for?
Solution 1:
I can think of two reasons:
By making the number of available clusters comfortably larger than the amount needed to upgrade everything, they can add new superpowers or enhancements to the existing ones via DLC without having to redo the map and figure out where to put additional clusters.
It means players can max out their superpowers without having to pixel-hunt the entire map to find out where they missed a cluster. Probably an important consideration given that they're not marked on the main city map and the minimap's range is pretty limited...
This is conjecture on my part, obviously , but I think they make sense.