You want to breed for a hardy horse, not necessarily a showy horse, right? I'd like to see recent pictures of the stallion, personally I don't think he's bad. I did first notice his bum, but I don't see it as a problem as much. Although I did grow up with cow-type, working quarter horses so I'm a bit jaded towards being bum high, haha...
That filly is really bum high, but she's young, and once again, it's not something I see as a problem to deter you.
I understand what you mean, every breed seems to be going for that flashy showy light boned type, less of the heavy workers now.
The issues that seem to be coming up all seem like they're issues that depend on the person, but don't really matter. I think that if you feel like this is the best stallion, go for it if you're ready. Breed the best horse you can for YOU, and if the looks aren't the best, you can work on those later, when you KNOW you have what you want in other aspects. Because the whole point in this is for a horse for you, to continue breeding to make the horse that's perfect for you specifically, right? Not one you plan on selling or making a profit, so being up to anyone's standards but yours doesn't really matter, IMO. If your mare is proven to have good performance and works well for you, despite her faults, and same for the stallion, you'll be fine.