Following the principle that one should compare the two players when one of them was a year and a couple months older than the other, instead of comparing the two when one of them was just a couple months older than the other (in which case Matthews would have come out ahead in points both at ES and on the PP).
No comparison is going to be perfect. If you use Malkin's rookie year he's losing out on experience, which is huge for a player, especially one who didn't play in North America. Malkin made a big leap in his second year, and showed greater improvement than Matthews did in his. The assumption that any player who is better at 20 is more likely to continue to be is incredibly flawed and one of the major reasons why scouting is so difficult. Their production at same ages is certainly worth considering, but not at the cost of ignoring what Malkin became.