I'd like to elaborate on this and share our policy regarding stats and scoring:
Lets say I have 3 of one pet: 23 Uncommom, 20 Rare and 15 Common. Which is being counted in the average?
The 20 rare.
Our scoring system (and by extension, the stats) is weighted to reward quality more than level. This was done because pet leveling can be gamed (i.e, capturing duplicate pets at the highest level of any quality). Collecting better quality pets cannot be exploited -- you'll need to actually farm for rares or choose to upgrade certain pets.
Our goal is to have each pet count only once. If we were to count the highest rarity AND the highest level (i.e., count two different versions of the same pet) then our scoring system would be open to exploitation. People shouldn't collect pets simply to max their pet score. Rather, their pet score should be a reflection of the best pets in their pet collection. As far as we're concerned, quality trumps level.
The bottom line is that if you're looking to maximize your score, level those pets of the best quality, or upgrade your highest level pets. You can't go wrong with either of those strategies.