99 doesn't mean they are Babe Ruth or a perfect player. It just means they are a 99 at the position they play and that is the highest number the game shows you. The best players cumulative rating ends up being closer to 120. 99 is not an average by any means. I don't know why people make things so much more difficult than they need to be. Your idea of a 99=/=the game's 99. MLB The Show doesn't use its ratings like NBA 2k or Madden.
If they wanted they could make 130 be a 99 and scale everything else down. I am sure people would complain less. They could also say 200=99 and scale everything way down to where the average player is like 30 then people would freak out. It is just eye candy. It'd be the same exact results regardless of the little number next to their name. The individual attributes per player do not change one bit. Look at the 99 rated pitchers. None of their per nine attributes, control, velocity, etc. is even a 99. Settle down people.