Negative upgrades exist to limit how many positive upgrades you can get. If you get unlucky, you'll be forced to take a negative. Positive upgrades also get rarer every wave beyond wave 10. They exist purely for balance.
I'm assuming by "intro" you mean the tutorial. The tutorial only appears the first time you start the game, and even then you can skip it. I suppose if you're playing on HTML with cookies disabled it might get annoying, but other than that I'm not sure.
