The premise of different challenges that test different mechanics leading to different kinds of upgrades is clever. It seemed like you were on the path of having each speedrun unique both in gameplay and reward, but then you didn't dive fully into that.
The most interesting upgrade to me was the one with a multiplier based on how much you completed speedrun 3 (save wiped, forgot if that was exactly it). I think the game has a lot of potential if you continue leaning in that direction, so that your various speedruns feed back into each other and the different challenges evolve over time in how you handle them. You already have a bit of that in your upgrades so you're not too far off.