There are excercises for stregthening ankles, I probably got a list of them somewhere around my room...
yeah, my ankles and knees are effed up too. doesn't stop me, pretty sure i broke something in it about a month or two ago and it hurt quite a bit but eh. i have a wobble board, that helps, and constant stretching so you're not putting any strain on the ligaments & muscles. also, it helps to stretch out your calves and legs too, because having those muscles loose reduces the pressure on your ankles.
source; a lifetime of lower leg problems, including but not limited to, shin splints, extremely sprained ankles, potential broken foot, broken toes, floating bone, the list goes on :|.
anyways, you don't want to build that much muscle, trust me. i have beasts of calf muscles and they piss me off. if i stretch out my leg and point my toe you can literally see about four dents in my leg and my calf muscle is like a proper corner. i hate it.
cycling on a lot of resistance will make your bum bigger, squats aren't too bad for your ankles at all. but it also works on the top of your legs and not really the bottom that much. i'd recommend skipping, you can potentially hurt yourself but if you don't do anything your ankles will just get weaker and weaker and you'll end up never being able to do proper exercise. take a risk and it will strengthen them a lot.