I dunno, I kind of think it works well. In my case, I've taken away the destiny point cost, but I did make it so you can only change jobs between sessions, as we play weekly. I know you could pretty much swap jobs at will in games that use them, I don't want my players changing jobs every 5 minutes. The only thing that really bugs me is that you lose your innate ability and it's replaced. I haven't come up with an alternative, but it seems kind of meh to me, at least from somebody who comes from Pathfinder/Star Wars Saga Edition. I kind of like the way they multiclassed in SWSE, you only got one of the starting feats, not all of them. So perhaps instead of replacing the innate ability, you retain it, but then you don't pick a new one. YOu simply get the new innate ability.
So going from Dragoon to Engineer, you would keep Jump, but rather than picking a new ability you only got Invent, and all the math for hp etc, stayed the same.