I've got three sons and a step-daughter. They're all challenging in their own ways (except my youngest, who I consider God's gift to me for managing the other three). I find that boys have more "issues" with developmental delays and school problems. If you have a boy, you are much more likely to deal with speech delays, learning disabilities, ADHD and the Autism spectrum. Not to say that these don't affect girls, or that girls may not be under-diagnosed and boys over-diagnosed, but I think that in terms of acclimating boys to societal standards in general and school in particular, those things are a better fit for the way many girls are wired. So the difficulty with boys, IMO, comes from this very weird place in society that we're at right now where some traits that are stereotypically male seem to have lost value in society and where being "all boy" equates to "all trouble" in the eyes of many. It also seems that many young men no longer have a place in the world to find fulfilling, steady work in a field that doesn't require a college degree and not everyone is college-bound.
My experience with my SD is atypical in that she was in an abusive home with her mother so she's overly compliant and doesn't push back much, but my girl-mom friends certainly seem to have their hands full with their daughters and the drama and mind games. That said, most girls I know do seem on the path to successful lives - most I know are good students and active in activities, community service and leadership and seem to gravitate towards that on their own. By contrast, most of the boys I know would rather play x-Box and eat pizza all day than organize a toy drive. Many of them seem a lot less ambitious than their female peers, so it will be interesting to see them 5 years from now and see who is succeed in college and who is living in the basement.
At the end of the day, I'd take boys over girls but that's probably more my boy-mom bias than anything else.