The comparisons are strained at best; they're completely different films, ideologically, and even on technical grounds the comparison is unfavourable to Nolan. Bruce Wayne = Michael Corleone? I don't see it. At all.

The Godfather works both literally (plausible, psychologically sound aesthetic) and allegorically (the grander themes of family, justice, betrayal, revenge, etc.). The Dark Knight is pretty thin in both respects, and critical attempts to adultify it seem unwarranted, unnecessary. It's a decent action film, perhaps the best so far this year (I still haven't seen Iron Man, which looks much better).

I find the notion of putting it on this sort of serious pedestal a bit silly, anyway; IMDb's Top 250 takes its votes from a very selective demographic. It wouldn't surprise me in the slightest if half of the voters who put The Godfather up there were only doing so out of some sort of attempt at objective canonisation.

(And canons are inherently elitist and conservative anyway.)