The way to get more accurate grades is to have an average for each instructor, you could say for instructor X his average score is 30 for BIs and if the stud earns a 33, he would net three aboves. So essentially every instructor would have their own personally tailored handicap. Of course when you have a new IP you would just have to use the squadron average for the first few flights to give him time to build his own average.
For every scrooge, there's a Santa Claus. Also, not everyone gets to fly consistently. That's not "fair," either. Guess what, such is life. Lastly, again, a scrouge will "hinder" your grades a bit, but in the end, if you meet MIF (which, once again, is different than getting a 4) sooner than later, that's what matters. If you're not that good to begin with and only hit MIF at the end of block, then having a scrooge isn't your overall problem (which is not to say that you won't make it through the program, it will just be harder).