I play this game like I'm addicted to it (maybe I am?) and I've always used an Xbox 360 Controller...until recently. The reason why I decided to give the M/KB combo a try was because I wasn't able to see everywhere like I want to in challenge maps where you fight a lot of bad guys; for instance I'll kick guys all over the level so they're spread out, but because of that I can only see so many of them. I knew that if I used a M/KB setup, that problem would virtually disappear since I could move the mouse to look around, instead of using a thumb stick to when I should be pressing buttons.
Of course when I decided to try this, I went with my own custom key mappings, since the defaults are always weird to me. Shortly after sticking with this combo, I beat one of my scores on a challenge map; the previous score was 77000ish, and the new one was 78000ish. So while it wasn't a huge difference, I knew this was what I was going to stick with since it felt so much more natural to me, and I knew I would just get better with time.
With that being said, there are very minor quirks with using the M/KB setup that you'll come across while playing the story mode - for instance in some boss fights you'll have to rely on the keyboard to decide where you want to strike, when generally, you use the movement of the mouse to do that. Anyway, I'm a former game pad user gone M/KB, and I have no intention of looking back - even when the new Batman game comes out next month.
In the end, it's all just personal preference, but you won't know your real preference until you give both a try for yourself.
If you would like for me to show you my M/KB binds, I will be more than happy to post them for you, just let me know.