The mastery system means nothing, but is a cool way to get free stuff. Statistics don't paint an accurate picture, and no matter how complicated you make a framework, a static appraisal is flawed.
For example, you could have the highest damage dealt, and most CS on your team as a Varus or Ezreal and still be worthless overall, since you weren't using the damage properly. Suppose you didn't commit to fights, and your team always died with the enemies at 2%. In contrast, assassins could have among the least damage dealt to champions, but be the MVP because they eliminated priority targets effectively.
About what I said about making the framework complicated, you could try to count "clutch heal saves", as in "healed a target at under 5% HP" or something, but there will still be too many nuances to know whether or not a particular play was good in that context. In this example, the heal could've been on someone who was going to die regardless, or whose life didn't matter at the time.
I've had games where I played ridiculously well, making plays all over the place and still gotten a B+. Even my stats painted a decent picture in a Thresh match on ARAM. Meanwhile, in another game, where I didn't play as well, I got an A+ because of whatever. Making this "whatever" clear, would be nice, but it would be abused. It also cannot be a good guideline for how you should play.
All that said, in many cases, the system does work, because the stats do have a lot of correlation with victory. Just don't read too much into it.