I never felt that Val Kilmer or George Clooney were very good choices as Batman - and it had nothing to do with the script. They never seemed to have the dark, brooding qualities I always associated with Batman (60's series aside). They seemed a little too happy-go-lucky. They never struck me as a character that really had a dark inner side dealing with the emotional loss of his parents.
I think the casting choice of Michael Keaton may not have always worked, but I think he pulled off a better "Batman" overall. You're right - he didn't seem to have the athleticism of some of the later choices, but he did have some of the multi-dimensional qualities unique to Batman. Maybe it was the mood of the first film, but Keaton seemed more deeply troubled, and genuinely like the dark knight. Keaton played a more subdued (comparatively) Batman who was the product of his past.
I enjoyed the score – but unfortunately I’m starting to get Danny Elfman’ed out. All of his movie themes are starting to sound alike… Maybe it is the “John Williams effect” in effect.
Finally - who could forget the Joker? Jack did a great job, making the Joker a believable (and arguably) and the most disturbing character in the Batman series.