I dont recall exactly what upgrades I picked, but I know that on my first run I picked a variety (such as the one that has explosions affect surrounding bricks, and the one that lets a ball pass through bricks) but on the run where I shattered the core, I stacked the upgrade that gives extra balls.
As for the wave, I think it was 13, but Im doing that from memory and it may be incorrect. It was only a single wave where I had the opportunity to shatter the core.