The Reader pretty much only got in by default, since it's a weak overall year and the superior nominees all have some sort of arbitrary problem.
1) The Dark Knight is a comic book film, and as such can't possibly hold up in the Academy's eyes. We'll have to wait for them to evolve first. The Academy, not the films.
2) Very similarly to point #1, Wall-E is an animated film and faces that same stigma. Not only that, but unlike TDK, it had even less of a chance to begin with because it already has its own Oscar category.
3) The Wrestler is very stark and realistic in its depiction of violence, as well as a number of other things, and Academy voters are generally prudish. It's also not a "sexy" pick. Tiny budget, very documentary-like feel, and it's about a professional wrestler.
Kate Winslet beat herself out for the Lead Actress nod, with The Reader. And DiCaprio would've had an uphill climb into the Best Actor category - there was pretty much just one open spot, and it went to Richard Jenkins, who was awesome in The Visitor.