Ah, but Jack Black hasn't portrayed the love interest in as a dramatic movie as this. Usually those actor's play those roles and it adds to the humor. I'm not saying Maggie has no talent, nor am I saying that the role just needs a pretty face. There are several attractive and talented actresses out there that I think would have made more sense.
And it's not just a guy thing, because the two people that were bothered more by it than I was, were my sister and my wife (my sister actually said that Gylenhaal distracted her from the story because she just didn't buy all these men fawning over her).
It doesn't change how brilliant this movie was or take away from Maggie's talent level, or that Batman can't be above "looks." If she wasn't the love/beauty interest for every guy in the movie, then it wouldn't be a big deal, but that's how the role was written.
However, beauty IS in the eye of the beholder as you say, and we've all got different eyes. So, those that find her attractive won't have an issue with it.
I personally wouldn't have mentioned it if I thought she was at least moderately attractive. As it is, I think she looks too much like Skeletor's little sister....and unless it's a comedy, that look doesn't work as the beauty for me. So, she's kind of my anti-type.
I guess, to be fair, I'd be just as upset if they cast Steve Buscemi as the next James Bond.