Why was Christian Bale so much leaner (less muscular) in the TDK compared to Batman Begins?

I actually never noticed that. Maybe it was because of his very fast weight gain he had to manage after he finished filming The Machinist?

8 years had past by the time TDKR came around, as for TDK I guess the explanation for his muscular body in BB is because he just got back from Bhutan where he not only spent time training with Ra's al Ghul which most certainly bulked him up, but he also had to fend for himself and even climb mountains, by the time TDK came around he hadn't had to to do that for quite some time.