BTW, wrote this before seeing Dargno's post above (basically the same method stated slightly different)
I think part of the problem is that the number IS a multiplier of an average. As Blizz adds pets, that number (and the hours spent leveling) has less and less impact on your score. For instance, if there were only 100 pets in the game, and you had all of them, it would take a total of 25 pet levels to gain one point. With 500, it takes 125.
Perhaps a better method would be to use Total Pet Level / 25 (or *.04). This way, no matter how many pets Blizz adds, you can always get a point by gaining 25 levels and the hours spent leveling pets always contributes the same amount to your score similar to the way a battle stone always contributes points.
This would be the same as avg level * 4 @ 100 total pets
Each individual level 25 pet would contribute an additional .96 points over a level 1 pet (.04), similar to the way a rare contributes 1 point more than an uncommon pet.
This would give current players with 500 pets a boost of up to 400pts (realistically more like 240), while taking away slightly from those with < 100, but allowing them to gain points evenly as they level new pets.
You could of course adjust the multiplier of .04 to make leveling (or capturing higher level pets) more significant to the overall score. Say .08