It's a goofy, fun arcade game based off a goofy, fun comic.
However, this is Initial D, not Forza or (god forbid!) Gran Turismo.
Naturally the assumption would be the 300hp car would beat the 140hp car uphill, and you'd be right. I'm going to assume you were playing against the CPU, so perhaps driver isn't as much of an issue in this case. Handling isn't the only thing that can determine whether or not that GT-R beats the MR2 (I assume you mean a MR-S? I don't know the MR-S chassis code) uphill the engine performance (read: powerband and acceleration) and the driver play a huge part as well.