I would lunge or free lunge, TIME, and whatever everyone else says for nutrition. I would only add probiotics to the list. I have a 3-year-old stud colt with a pencil neck. It's driving me bananas. His problem is adolescent "uglies" and the need for more pasture time. I plan on gelding him, but I am going to wait until he fills out more. In my years with minis the age 3 is the "uglies" age. None worst, not even yearling ganglies. Year 3 uglies and whatever year the tooth bumps are worse. It always alarmed me because I came from a world of large horses where you never noticed teething.Tell yourself it too shall pass. Also, exercise is the absolute best thing to do to beautify a horse. All of the magical supplements in the world will not go where exercise can take you.
I would also second deworming. I always used ivermectin, but you will eventually find the need to rotate with something that will treat tape Spring and Fall. Pilates/yoga for people and exercise/dressage moves for horses. You will find that minor conformation defects will correct. You could even go so far as lunging with a bitting rig, as long as you do the training gradually. If you have heard the 3 days, 3 months, and 3 years saying for conformation critique, with minis I'd almost wait for year 4 for everything to even out. Almost all of mine were about at their mature height at two but they don't fill out completely until 4. Only one of mine had calcified tooth bumps. The rest the facial swelling and toothbump appearance was gone by 5. Best of luck!
