Thank you very much for the detailed feedback! Really glad you enjoyed the game.
To answer the question about the upgrades: they do persist between pickups so you should feel free to swap as you wish. I don’t think we conveyed this clearly (we added very subtle 1pixel different colored upgrade indicator sprites that stack above each shoulder to display current upgrade level) it’s definitely something we need to rethink if we ever decide to keep iterating on the idea.
Boss AI should probably be tweaked to prevent the scenario you describe, but it should be possible to lead him away during a certain phase? Maybe not though.
thanks again for this awesome feedback! We loved runelite, just so you know!