I train several competitive cheerleaders in that age group. The first thing you should do is use something like the FMS to first locate any imbalances. The first step is to put in place the corrective strategies for whatever the FMS revealed.
Following this you have to consider what your athletes job is on the cheer squad, are they a base or a stunter. This effects what they are doing most in practice. Once you learn the demands of their spot on the squad I would try to go to a practice to get a feel of what they do there. This way you are helping their progress and not being counterproductive or doubling up what they do there. This is the only way you can safely write a program that will keep them progressing.
The one thing I would definitely put in place for any young athlete without knowing specific abilities is scapular stability exercises, core strength, lateral line strength, and flexibility. I would also then spend a lot of time teaching them how to control their body through basic movements, squats, push ups, get ups, lunges, planks, and stuff like that. I would avoid most plyometric impact exercises because of the amount of jumping the are doing at practice, with the exception of jumping up on to a box while emphasizing a soft quiet landing and stepping down, never jumping down. This will help to teach them to land properly and make the high impact the sport demands a little safer.
The best way for us to make better athletes is to help keep there bodies ready for the impact of their sport so they can practice their sport. If we get too crazy with the exercises we raise the risk of injury, causing them to not be able to practice. This would be an injustice to the athlete.
I hope this help