Malkin just hasn't had the year-to-year consistency that Crosby has had. Omitting the current season:
Top 10 Points Malkin
2007-08 NHL 106 (2)
2008-09 NHL 113 (1)
2011-12 NHL 109 (1)
Top 10 Points Crosby
2005-06 NHL 102 (6)
2006-07 NHL 120 (1)
2008-09 NHL 103 (3)
2009-10 NHL 109 (2)
2012-13 NHL 56 (3)
Top 10 Points-per-game Malkin
2007-08 NHL 1.29 (3)
2008-09 NHL 1.38 (2)
2009-10 NHL 1.15 (8)
2011-12 NHL 1.45 (1)
Top 10 Points-per-game Crosby
2005-06 NHL 1.26 (6)
2006-07 NHL 1.52 (1)
2007-08 NHL 1.36 (2)
2008-09 NHL 1.34 (3)
2009-10 NHL 1.35 (4)
2010-11 NHL 1.61 (1)
2012-13 NHL 1.56 (1)
And I think most people agree that Crosby's non-offensive game is better than Malkin's
Oh, I agree but there are interesting factors such as first all star teams (3 vs 2), Art rosses (2 vs 1), Conn smythes (1 vs 0) and Harts (1 vs 1).
And while Crosby plays a very high energy game and is better defensively Malkin is not a bad defensive player and is very good at takeaways. You could also argue that while Crosby has had injuries that has made him miss games, Malkin has had injuries that influence PPG more (shoulder, knees vs concussion, jaw).
They are close as post season players and are their top 10s really that far apart. If we would take away their equal finishes it's 1 vs 3, 3, 6 (and one of the 3s were in a shortened season). Make it top 20 and we get 1, 18, 19 vs 3, 3, 6 (with one of the 3s in a shortened season).
Malkin also finished as a clear 3rd in the KHL point race with considerably less games in a lockout strengthened season. I think that should also be accounted for as impressive.
They are also close in Pitsburgh MVPs (3 vs 4 in favor of Crosby).
I agree Sid takes this (mainly by his per game dominance) but I think the above shows that you could make an argument that it should be somewhat close. Malkin has consistently been ranked as one of the few superstars in the league for most of his career and let's (for arguments sake) say Malkin beats Crosby in the art ross and Hart race this year (which is not an unreasonable scenario). What then?