You also have more girls who are competing both in high school AND in all stars. These two seasons overlap as far as practices are concerned and many girls compete at region and state on Saturday, then turn around on Sunday and compete with their all star teams. In most schools, girls are still cheering for football (even if it's just for home games) during the fall simply because that's the way programs are still being maintained. The skills required have definitely contributed to increased injury, and this is coming from personal experience; I competed on wooden floors (when state was held in Macon) when having a tuck was considered elite. Here's something else to consider: after any type of injury, there is going to be necessary rehabilitation in order to truly recover. There are many who consider that slapping a brace on and that's it. The continual use of braces without proper rehab and recovery is going to hinder rather than help. Face it- you've got kids (and parents) who want to compete, regardless of what consequences they may face as far as injury is concerned. When you can go to Walmart and buy a brace for any body part imaginable, you're going to see a lot of braces, many of which are unnecessary and do not help as intended. I had a girl once who came in wearing a knee brace because she had told her parents about a pain that she had in her leg, They went to the local pharmacy, bought a huge brace, and she thought she was going to wear it and all would be well. Turns out, she had a charley horse. So, not to disregard the legitimate injuries and braces, but some are serving no purpose whatsoever.
As the demands and skills increase, so will the injuries. I don't think that it has anything to do with a shorter season, because many of the girls are going to cheer year-round anyway with all stars, as even all star programs are starting their practices earlier in the year, as well.