Here is a photo of Isa Danne riding Xato, a 5 year old Lusitano, at the Paris Horse Expo last december. I love the freedom of the movement of the right shoulder.

Many problems come from the horse working with tensed shoulders.
Like a human used to hold himself in a incorrect posture, horses can get used to work in a incorrect position and therefor develop chronical tensions. It may also be a trouble in the proprioception - the representation of one own's body.

When you ride (on a circle or throught a canter transition), try to get a feel of the shoulders in your hands. If you feel a heavy, awkard, tensed shoulder, you may have to re-educate the shoulder to functionnate correctly.
Focus on exercices that demand bigger movement from the forehand and focus and getting a big, smooth gesture from the shoulder. Do them at the walk to control the movement in its whole and don't accept any tension anywhere in the body - especially ask for the horse to chew his bit.

Shoulder-fore and shoulder-in are obviously good ; start with a small angle, but within weeks, don't hesitate to ask for a bigger angle. Start from the ground if your horse is not familiar with this exercise because you don't want him to learn to do it in a tensed posture, and it' s more easy to control and correct everything from the ground - and it's also less stressfull for the horse.
Turn around the hindlegs are very good. Start also from the ground if you have difficulties.
You can also ask your horse to stick his head (just his head) to the outside of the circle while getting also the hauches on the outside. Focus on keeping the inside shoulder on the circle, as the shoulder controlling the shape of the circle. Keep the horse relax, and just do few steps at the beginning ; then straighten your horse on his circle ; then ask again ; then change hand, etc... This exercise that I got from Isa Danne is fantastic and is called in french "les deux bouts dehors" - "the two ends out". I love the fact that the inside shoulder has to be so strong and holds itself ; but be also careful to get a good activity from the outside shoulder.
This three exercices are quite easy to perform at the walk to start freeing the shoulders. Go to the trot once you get a better feel of the shoulders of your horse - you're on the way out of the main problem and now can start the common gymnastic of dressage.

To finish, the best exercise I've found to reeducate a shoulder was with a mare that had surgery on her shoulder as a yearling and sincethen, kept walking from this leg without lifting it, but with balancing it to the side.
I taught her spanish walk and this really changed her life drastically !
Within a few weeks, she even jumped over 1 ft for the first time of her ridden life (what was impossible before) !
Sometimes, you have to explain and show to your horse that there is a better way to move his/her problematic leg.

Same can go with a horse that has trouble engaging one of his hindlegs.
A problem that your vet cannot really spot can be just a bad habit from your horse.