I like that the shooting spread upgrade makes it desirable to get very close to enemies to deal damage. OP upgrade stacking isn't as much of a problem in this game as it is in others since they get turned off while charging.
Edit: In that regard, the hull upgrade is the most over powered, since when at a high enough level you literally cannot die just holding space. If the excess hull beyond the initial amount was temporary it could resolve this, albeit with the caveat of making it even harder for less skilled players.