Re: ridiculously low improvements of upgrades upon the characters
First of all: these upgrade do make a difference. You may not see it but it is there. It also depends on your play style.
Take a Scientist for example. He got 100 HP and 110 with the upgrade. Why does that matter? Because with 110 he can survive a critical hit from a Future Cactus which does 102 damage.
Secondly: it would not be fair to have a bunch of high level players, with many hours of experience in the game, have access to powerful upgrades no newbie can compete with. It would simply ruin it for newcomers when they literally need upgrades to succeed. So what we got is a mix of potential upgrades and fairness.
There are a few characters that perform better after certain upgrades, like Rose with her homing for example, but even without and the right play style it is possible to succeed. Even more so as a team.