In my opinion, TDK overshadows BB because BB is an origin story. To most movie viewers, i.e. those that don't follow Batman of Nolan, learning the intricacies of how Batman came to be is not as "fun" or "cool" as watching him really coming into his own with the gadgets and the villians. Overall, TDK is a bit louder and more theatrical whereas BB is more of a narrative (not saying TDK isnt). I think that that's why it gets overshadowed.
I think truly the two movies aren't really comparable. They are two different movies that portray two different points in the Batman's life and, therein, you have the problem of Batman becoming more dynamic as he goes. For this reason: All other superhero movies ever>BB>TDK>TDKR. It's the only way it can work and make any sense at all.
Btw, I loved both movies.