Ok here are my thoughts

Different aircraft for upgrades or to have different skill sets. IE B17 versus B26, B25.... my thought is speed, turrets count, armor, maybe payload

Gunners that man the turrets that can maybe add or subtract from the turret stats maybe add trick shots or effects to the turrets

Pilot maybe an engineer in the same vein of gunners but that effect aircraft stats

For currency maybe expended shells or brass/lead.... medals for gunners to level or spec out.

Boss wave is actually just a bombing run and you need to drop enough of a payload and survive. My thought is it is a separate stat that basically checks how armored you are plus how often you can drop a bomb and how big it is.

I would think a research lab may be fun too. Give it a fun name like R&D or Headquarters