So I find myself in some agreement with the second half of your post. I really strongly disagree with the contract thing.
I think objectively what hurt Malkin's "story" (and his level of recognition) more than anything were the '09-'10 and '10-'11 seasons. Like, his first three years he goes on a rookie tear and then finishes 2nd to Ovi in Hart both of the next two years. Team goes to a finals and then wins a cup. He wins the Smythe. People had started to include him with Crosby & Ovechkin as a sort of "3 generational players" type group. Then he has two seasons where he kinda regresses, and in that 2nd season he gets badly injured after that collision with Tyler Myers. So like, he was in the Crosby/Ovechkin grouping but then fell off for 2 years, leaving that group in people's minds.
Then he comes back after that with his incredible '11-'12 and he has been really, really good - albeit injury prone - ever since. Until this year. Anyway, it was still laughable that he didn't make the list but I don't think it was a perception of his overall inconsistency. I think those two down years in '09-'10 and '10-'11 really hurt his recognition-levels.