I have tried Nodebuster (And finished it), and after a day of working on this game I realized how similar it was and then started to take inspiration from it (This is why I added a skill tree, but put my own twist on it with the enemies).
For the damage upgrade in from of the tankers, I think doing it in parallel would be a good idea, but for the upgrades after the damage & enemy, you would either need to have both upgrades to unlock the next upgrades, or have the enemy unlock a new branch of cool upgrades.
Also implementing more choices with completely optional upgrades would be very cool, I've had some people suggest paths that will lock another one (Someone gave the example of giving the saw a fire or ice upgrade, but you can only choose one)
Thanks for EVEN MORE amazing feedback!