Keep in mind that the scoring has evolved a little over the last few years. It used to be more heavily weighted for offensive players. Goals against scoring also used to be higher so that defensive players often ended up with 0.5 or 1 point frequently. The TK/INT was added to help boost that and the goals against was lowered. The only way defenders used to score well was with clean sheets.
I do agree that the saves is probably a bit inflated. The top tier goalkeepers are at 4+ ppg. Most others are between 3 and 4 with the lowest being 3. The lower end is probably a bit too high. If we changed saved shots to 0.2 instead of 0.33, I think that would certainly help. But, it's only 1 position and it's a relatively minor change. More than that and I think things start to get skewed.
Points for shot on goal is interesting. I think that would be a reasonable addition (something in the 0.1 to 0.2 range), but I'm not sure it overall changes much other than adds another layer of scoring to what is otherwise relatively simple and that's part of the beauty of it. I think 0.5 pts for a SOG is too much, though.
Giving a point for a win seems like it would heavily skew the top end more than it is.
In the end, though, I think the current scoring system is way better than it ever was in the past and there's something nice in the simplicity of it. Once we start adding so many more variations on that, then it starts to get away from just enjoying the soccer portion of the league.