Why do you assume that they added more schools to the largest classification simply because they combined enrollment? One has nothing to do with the other.
Division 1 and Division 3 are going to have the widest ranges of schools, because they include the "outliers". That's pretty obvious - Schools of 2800 students are going to have an advantage when there are only, say, 15 other schools with at least 1900 students. Likewise, schools with only 5-10 students are going to be at a disadvantage when they compete in a classification made up of schools between 50-200 students. That's always going to be the case, and just because the classification is determined by the combined enrollment rather than gender-specific enrollment has nothing to do with that issue. If you want schools of more similar size to compete against eachother, then you have to further limit the number of schools in each classification, meaning you add more classifications. Separating boys and girls by enrollment makes no difference.
Traveling to multiple destinations for the same program/coaches/parents is a problem, particularly when there is only one coach. That means that those coaches would have to choose which meet to attend and which meet to forgo - a pretty serious problem if a team is trying to qualify for state, or even give their kids the opportunity to continue their season as long as they have qualified for the next level. Likewise, parents having to decide which son/daughter to go isn't exactly a great situation either. It may only happen once a season, but it's a very significant problem that doesn't need to even be an issue in the first place.
Population has quite a bit to do with unequal representation. A county with a student population of 50,000 is going to have less kids than a county with 500,000 students. Likewise, a county where most high schools have enrollments between 100-400 students is going to have fewer representatives at the Division 1 level than a similar sized county where most high schools have enrollments between 500-900 students. The only other reason for uneven representation, which you mention, is that some coaches might be more successful at building a boys program than a girls program at the same high school. That's an issue you should take up with your local AD if you are really concerned about it, as obviously a coach's first job is to have a team in order to compete.
It matters how many other divisions there are in different sports if you want XC to be treated the same as other sports. If there are, say, 8 divisions in football and 1 division in XC, then the teams are being treated differently in those sports. For one, there are 8 state champions in football versus 1 in XC; for another, more similar sized schools are competing against eachother in football than in XC (and isn't that the source of frustration in this thread, unless it's just to complain about a change whether it was for the better or not?).
In other words, all along Ohio has treated cross country differently than other sports. Why the outrage over yet another difference, when this difference does more good than bad (and is far less unusual nationwide)?