I'm not sure there's a definitive answer really. I guess you'd have to have the same option file in each one to really answer it accurately.
Then are the player's stats correct. And that's where everybody would have a different opinion on what stat number is right. Then let's say for example Messi would be the number 1 player in speed when dribbling with the ball at his feet, I think we can probably agree on that. So then where do you set him for Dribbling speed, does he dribble at the same speed he can run? Probably not but for arguments sake let's say he does, so he would have to be set at 99 for Dribbling speed and then everyone else would be somewhere below that down to a lumbering centre back.
I guess with top speed now being recorded that is a stat that perhaps could be used to rate players. Although it's a flat out speed so it could be argued a speed over a distance might find a different order but it would at least be a scientific based way of doing it rather than guess work. Using the gap from top to bottom you could work out increments to use the full 1-99 on the Speed rating. That would (certainly in retro one's) really show up individuality. So taking this page...
http://www.espn.co.uk/football/blog...yers-man-citys-leroy-sane-breaks-speed-record
Obviously that's just one league so you would need all but using just the Premier League Sane would be 99 and whoever was slowest you could set at a low figure and see how long they take to cover half the pitch and then set that figure as the low stat and put everyone else in between in increments between the top and bottom recorded speed.
You could use passing accuracy for short passing too.
I seem to have wandered off a bit here so I'll stop!