You have 2 takes on the same character, with 2 different actors performing them. How could you not compare them?
The fact they're vastly different in execution isn't really relevant. Ultimately, each one attempts to portray Bruce Wayne/Batman in a certain way, and will do so with varying degrees of success. And that's why it's fun to compare them - to see which had most resonance with the viewers.
I love both films and will always hold a candle for Batman 89, having gone to see it in the cinema on release with my dad. But I agree with Thefuture above - I never really got to 'know' Keaton's Bruce Wayne. He played the character as the strong silent type, and asides from Napier's involvement in the death of his parents, there wasn't much backstory to the character. Where did he learn his skills? Why does he keep doing it after Napier/Joker is dead? What was his ultimate goal as Batman? We sometimes get a sense of the rage and pyschosis inside him, but by and large Keaton keeps the performance toned down. There's nothing wrong with this approach - it suits Burton's gothic, stylistic film and adds a bigger air of mystery to this version of Batman. And of course, we have to bear in mind in 1989, audiences were still engulfed in the era of 80s action flicks. It was nothing strange then to have a male protragonist who simply did their job, and didn't dwell much on feelings and self doubt.
But on a personal level, I prefer Bale's version. His Bruce Wayne is engaging, more given to discussion and to sharing his thoughts with Alfred. Nolan gives us a story that explains how and why he became Batman, and offers forth a Bruce Wayne who isn't just a guy coasting along with this double-life - one who's prone to self-doubt. Hes a Bruce Wayne who's created this monster with an initial vigour and determination, but after seeing the consequences of being Batman, isn't sure if this is the life he wants. I feel Bale's version lets us see behind Batman's mask a little more, and in doing so, deepens our connection with the character. And I feel that Bale plays the roles perfectly : charismatic and suave as the public Wayne, introspective and determined as the private Wayne ............ and of course, agile, muscular and more than credible as Batman. Again this is more suitable for the demands of the modern audience, who are more prone to building emotional connections with characters and asking 'Why?', rather than just accepting what is presented to them on screen.