I guess I don't have any more suggestions other than to do what you can do - and add to it as you have the opportunity. Walking around with you in the arena is more exercise than she presently gets, so that is a plus for now. Since she likes obstacles in hand, see if you can add one simple obstacle as you ride. Build on your successes. Ask for one trot step after a low cavaletti, things like that.
As for "I haven't done much with her under saddle yet because I know how she's going to react." - I know this sounds new-agey, but picture her doing something different. Your body sends cues when you "know" what's going to happen - so "know" something positive will happen (within reason, of course) and work from there.
My gaited horse is VERY well trained. **I** trained her. She does more than follow another horse, and go in a straight line.
Mt horse types are very very easy keepers. It is where they came from many many years ago where the conditions were harsh with regards to feed, and weather. IOW there wasn't much to eat and they were worked hard. In the plow, to church, to town, by kids of all ages - which is why the have such sweet temperments. So they had to survive.
My rocky is a very easy keeper. Sweet, hard worker. She will go out on the trail with others, and by herself. She is the most sure footed, natural horse on the trail (like a duck to water) I have ever owned. And I have endurance ridden many years, and many miles. This mare is bold, and could care less if she is with others. We are a team together. Not her and another horse.
I have 2 horses. I do not keep them together all the time. I move them from pasture to pasture, I have 4 pastures. Just so I have no buddy sour issues. They see each other over the fence, go together like peas and carrots when together. This works for me.
Your horse just doesn't feel comfortable out by herself. But you know that already. Sounds like you have a start already by getting the two separated. I cross fenced my pastures just so I would not have that issue. They do go in different pastures, and get swapped around.
Gaited horses rarely receive any training, in fact most of the farms I've been to didn't have any sort of arena. Their "training" involves putting a saddle on the horse and having it follow another horse down the trail, which sounds like your pony. I'm pretty sure she's never been ridden in an arena. You're going to have to start all the way back to the beginning and treat her like a green horse, which she is.
Rarely aye? ha ha In fact, ha ha.
Wow such a broad statement for the mt horse breeds.
I have been to MANY farms. ALL had arenas. They may not be huge fancy arenas, but they had a place to ride.
This breed is bred to be a trail horse.
BTW my Rocky is *very* well trained. By me. Using dressage principles (gasp). She is *very* good on trails too, can do all kinds of obstacles also. I breed certified her too.