why not have upkeep a function of ONLY fleet supply research, and not fleet supply research AND income?
An absolute cost, while perhaps more realistic, wouldn't work well and probably wouldn't even be implementable.
Think about, how would you balance upkeep against variable resource incomes. I might have 40 credits per second income, 2 metal per second, and 8 crystal per second. Meanwhile my opponent has 20 credits per second, 10 metal per second, and 7 crystal per second. How can you possibly create a one-size-fits-all tax given these wildly diverging incomes? Similarly, the economies supported by maps vary dramatically. How can you create one upkeep cost that won't cripple someone with 30 credits per second income but is still meaningful for someone with 200 credits per second income? Can't be done.
It may not be realistic, it may not be popular, but I'll stand by upkeep for what it is: one of the best features that adds strategic depth to this game.