Let's leave aside the question of whether there is a "war on boys" or a "war on women," or whether the system is stacked against one or the other. It's clear that, regardless of how "the system" is "stacked," boys have significant problems with school as currently structured.
A better question, then, might be: how can we structure school so that boys tend to excel?
Here are a few thoughts on structuring a program for boys, with a very small amount toward the end on how it would interact with a program for girls.
1) It would involve longer school days, but with more and longer breaks for physical activity. Boys at the elementary school level should be getting up for a good forty-five minutes' play at least three times during the school day. At elementary levels one of these play periods can be formalized, into sports or (especially) martial arts; the others should be free. At higher levels, first two and then periods should be formalized: as boys grow into teenagers they need more structure to keep them out of trouble.
2) It should assume that boys mature more slowly, and thus focus on topics earlier in their education that require less emotional maturity. Math and science are good subjects at early ages; history and emotionally-difficult literature should be pushed back. Stories that can be read to boys, or that have shown a long history of being interesting to boys, are good at this age -- adventure tales, Robin Hood, or books without emotional content like stories about airplanes and trains. Stories that require them to confront or examine complex emotional truths are for later. The technical skills of reading and basic composition do not involve much emotional weight, but advanced composition -- because it requires a mastery of content, which comes from emotionally laden things like history and literature -- should be pushed back as well.
3) This implies that boys and girls should usually be educated separately, although the implication is not rigid; and in addition, there are substantial benefits to having boys and girls working alongside each other from early life. It would be good to break school days into class periods for each subject, and the classes taught differently, so that individual accommodations can be made. A boy who matures unusually quickly may benefit from being introduced to more emotionally complex materials, so that he might go to a class mostly filled with girls for the literary period; a girl might not develop as quickly, and go to a class filled mostly with boys. Because boys will focus more on math and science early, those classes will probably advance faster; some girls who show especial aptitude may spend part of their days in boy-heavy classes.
These are just some initial thoughts; any or all of these thoughts may be wrong. The point is to think about the problem from the perspective of trying to construct a solution that will work for the boys. What do you suggest?