I agree that the mastery system is busted. It counts way too strongly for statistics that are skewed away from early game, which makes it harder to get high grades in stomps that end in 15-30min.
e.g. cs'ing is significantly easier post 15min. Not only do you have the stats to insta-clear waves, but you also have your boots finished to get back to lane faster, have the strength to do random jungle camps, etc... damage dealt to champions is easier post 20min. Not only are teamfights more prevalent, but you again have the build in place to deal that damage. Yet I feel like these stats are adjusted linearly to game time. Which means a 60min slugfest can result in people getting S ranks everywhere (even though no one played amazingly since the game was so tight clearly) and 20min stomps where a few players do exceptionally well no one can get an S.
Oh, and kill participation. That's the worst one. Way easier to have 70% or higher kill participation when all the kills happen in teamfights. Really hard when you and one other laner and stomper your respective lanes and each only have 50% because you're not involved in the other guy's kills (and then less, because your jungler can just camp the third lane).