In short form, it really depends on what kind of story you're in the mood for, or what characters you feel like seeing. I can't call one better than the other, but I tend to watch Begins more often because that story is more personal and meaningful to me.
There are other little factors, like I think it might also have a tiny bit to do with Maggie replacing Katie. I really didn't like Maggie for the character, to put it gently. Also to be noted was the role of Scarecrow- Cillian did such a great job acting with just his eyes sometimes in Begins and I really appreciated that, as well as the sort of smooth, creepy intelligence of his voice when he spoke to anyone, the way he opened the briefcase. He was on his game, it was so fun to watch him knowing that he could crush anyone's mind he wanted at any time. In the second movie he's just kinda washed up and knows it, goes down without much of a fight. That was a bummer for me.
He does have a decent line though, and I guess it makes sense from a character development standpoint as well as getting the movie rolling without upstaging anything that was to come -- although I doubt there was any way to upstage the TwoFace and Joker stuff with a more badass Scarecrow bit at the beginning, but I digress..
So yeah, I guess there's no weighing technical ups and downs for me, it's all personal preference. And, needless to say, I cherish both films regardless.