I just registered to reply solely to this thread.
For the past two years I've been arguing with everybody I know on this topic, and my passion for what I feel is as present as it has always been.
Batman Begins is by FAR superior to The Dark Knight, in every way possible. Here's why.
To start, Batman Begins wins wholeheartedly in the narrative department. Whereas The Dark Knight was full of cliche Hollywood scenes that I saw coming from a mile away, Batman Begins spun a much more complete story that had me connected at every turn. Almost every scene was perfect for me. The murder of Bruce's parents was gorgeous and heartbreaking. Bruce Wayne's journey into the mountains to find himself was inspiring. His dialogue with Raz during his training was brilliant. Bruce's trip back to Gotham and his search for vengeance was genius. The reveal that the real villain wasn't Scarecrow at all, that he was simply a pawn for the League of Shadows which connected all of Gotham City and Raz was nothing short of stunning. Add all of this together with Nolan's sharp eye for cinematography, and I swear it was love at first sight.
Furthermore, I felt the Gotham City in Batman Begins was far more involving than the "Chicago" in it's sequel. The Gotham in Batman Begins was fresh, unique, ALIVE. The Chicago in The Dark Knight was the same old city you see in every movie of it's kind. You may argue that it allowed for betters shots of Gotham, and it had a less claustrophobic feel than Batman Begins. In all honesty, I just call it lazy. To that extent, most of The Dark Knight was lazy in comparison to Batman Begins. TDK felt like Nolan just wanted to make a Hollywood Blockbuster, and all the love he put in the first one was sapped in the process. What am I talking about? Let's take the scene where the Joker has the two ferries and has rigged explosives on both. That scene served absolutely no purpose but to put DEVO from Friday (yes I said it), on a boat with the chance to be a hero. I almost had a heart attack at how cliche it was, but I ultimately digress. Whereas Batman Begins had one emotionally involving and brilliantly written scene one after another, the Dark Knight just filled up most of it's time slot with one cliche scene after another.
And to top it off, and this really gets to me, the Batman personae Nolan worked so brilliantly to craft in Batman Begins was DESTROYED right off the bat in The Dark Knight. At the end of BB I was cheering with applause at Bruce Wayne's transformation into Batman, because it felt sooo believable, and I couldn't wait for it to be explored in future sequels. What does Nolan do? He throws in the character of Harvey Dent and has us believe that Batman suddenly wants to quit and have someone else take up his mantle. WHAT!?? Are you kidding me!? Didn't Bruce Wayne realize at the end of Batman Begins as his mansion was burning down around him (I adore that scene by the way) that we fall to get back up?? And that's what he did right, and he succeeded over evil? And the final scene where he tells Gordon that he would never have to thank him? I LOVED that. Batman was finally BATMAN. But for some reason Nolan destroys all of that genius with the random notion that Batman doesn't want to be Batman anymore, that he wants somebody else to do his job. WHY?? So he can throw in a new character to convolute the plot and lead to a 2 1/2 hour movie bloated with pointless scenes and unfulfilled potential? I was horrified at the end of my first screening of TDK, and I still am to this day.
The list goes on. I hated Maggie Gyllenhaal's character in every way possible; Katie easily was more likable (although I agree she can't act, but neither can Maggie). The Rachel character in TDK was annoying and ultimately irrelevant, the Rachel character in BB was much more complex and showed Bruce that, "It's not who are we are on the inside, it's what we do that defines us." I LOVED that. When Rachel died in the TDK, I honestly was just rolling my eyes once again. Another cliche, more potential wasted. The villains, with exception to the Joker obviously, were miscast and predictable. The scenes with Gordon and Harvey arguing were laughable. The whole technology of "Sonar Vision", or whatever it was called, was just stupid in my opinion and only served to fill up holes in the plot. Batman's voice was far more annoying. The movie was far too long and many scenes should have been cut off - Batman's expedition to China to catch the "squealer" had no purpose. The ending was predictable and completely inferior to Batman Begin's ending in every way. And I absolutely hated Gordon's monologue at the very end; it was cheesy and only served to show that Nolan was too lazy to think of a better ending so he had to TELL us why Batman was forced to run. Why not let us think for ourselves?
So, to end this rant, in all honestly I love Nolan and Batman Begins still stands as my favorite superhero movie of all time. While the Dark Knight was a good movie on it's own terms, and Heather Ledger was AMAZING as the Joker, when compared to Batman Begins it just falls apart in every way. You may think I'm over-exaggerating, or that I'm just crazy. Oh well. Batman Begins > The Dark Knight - ANY DAY.