I didn't have time to read through all the posts, so this could have been said already. Your lower body maybe too tense, making the canter feel rough. Lengthen your stirrups one day so that your leg goes straight down, so theres little or no bend, like a dressage riders leg. This will help you learn to use your theigh muscles, it will relax tense muscles and you would have stirrups to brace against. When you get on, sit up really tall, stretch your body upwards. Take in a deep long breath and exhale. While exhaling, relax and sink deeply into your seat. I find that doing this excercise really helps loosen up your legs and seat. Never grip with just your knees or calves. Big no-no. That can teach you to put your legs to far under you, which will hollow your horses back out. Do a LOT of sitting trot work with long sturrips. Think of being all loosey goosey. This is just an excersise and so don't worry if you feel like your flopping all over, just as long as you have control of youtr pony. If not, you may want to do it on the lounge. Make sure the trot is very forward, it will be very hard to sit (that means your doing it right xD) If you are getting bounced up out of the seat, that means your back joint (can't think of the name, the the joint right above your pelvis) is locked up and you are still tense.
If it is because your tense, it's a very hard habit to break.
Ponies do have choppy canters that are hard to ride, especially if he is on the smaller side. A lot of shortening the strides and lengthening the strides will help self carriage at the canter.
Wish you the best of luck!