The training we have started has mostly been short lunging work for about 15-20 minutes mainly to get him back into shape slowly. He has not shown any pain or issues with the actual work itself,
So... does 'no issue with the work' mean he enjoys
it or just does as he's told? I can't imagine running in circles for 15-20 mins(that's not starting 'short' IMO) is much fun for him. I don't actually think lunging is a great exercise for fittening - because it's just too tedious & boring - you can exercise their body, but their mind goes awol. I don't believe it promotes a good relationship at all.
he beats the crap out of my warmblood and I feel like if I ever moved my warmblood my pony would be happier about it. He is definitely the herd leader, but I have always been the leader of both of them.
Sounds like pony is a bully, and WB is rather insecure. How old is WB? How big is their paddock? Does/can he not stay out of pony's way? Just like a school bully who might have the 'obedience' of less assertive kids at a school, your horse may 'kow tow' to pony, and if he's the only equine company, he may feel more secure with him, but that's not synonymous with 'leader' IMO. And maybe you have always been 'the boss' but not seen as a 'leader' either. Maybe. Only speculating, but...
And I differ from Fox's opinion here, that I don't believe you can/should just force them to work hard to 'get them over it', whack it out of/into them. That will likely give you obedience - & if that's all you want... - but I want my horses to feel happy
about the 'work' I want of them, to enjoy it, be comfortable, confident to be with me.
If he's been recently separated from 'the devil he knows', when he was injured, this could well be to do with it - he thinks he's not going to be allowed back with 'devil' when you take him out. I've had horses like that. One of mine was the most independent horse I'd met. He was not a worry at all when mates came or went. He would actually leave his friends & walk over a couple of hills for miles alone, to visit a neighbouring farm with a lone horse(I found out he'd been making a practice of this when he was gone one day, that he'd been visiting at night regularly!). After taking him away to a (bad) trainer for only a week, he came back so stressed & frazzled, he still gets really
stressed if his mates are out of sight, worried even if they're on the other side of a fence! It took me a lot of work to get him back to the point of going out happily with me.