For the whole thing about upgrades will take away from the game. If you add anything more I would suggest maybe being able to buy startup items (dagger, double jump, and parachute) to have at the start or maybe someway to increase the max of the items. But nothing that would completely take away the skill aspect.
Head Researcher: I want you to make a flying waypoint that shoots electricity to make the space ship go faster for a second.
Assistants: Shouldn't we make parachutes for the ship?
Head Researcher: Just make the waypoints indestructible.