I don't get it... you find a wheel-less bag acceptable? I find the Hobie bag excellent, and my only problem is that my i12s fits in it too easily so I have to throw more and more accessories in it to keep it tight enough to stand up over the wheels.
The keel has to go parallel with the long dimension of the bag because the yak isn't compressible in this direction... otherwise packing would be a terrible strain. Of course the stern and bow have to be biased diagonally so their thick parts go side by side rather than atop one another. In the narrow dimension the yak is very compressible so squashes easily in the narrow confines of the bag. Stick pump, paddles, pfd, etc in remaining voids so the bag doesn't sag.
If I changed it, I would let the straps pull tighter in the longer dimension so I didn't have to add junk to keep it from sagging and dragging around the wheels. Maybe reinforce handle stitching, which seems strong enough but is pulled out of shape from use. I like that last strap which can suspend my mirage drive and the sailbag (I use the excess length of the latter to loop around and cling mast and all to the strap.
Surely there is some unusual factor in those problem bags, like a flaw or unconventional use? I just abuse it by having to carry it aboard rolled around the pump, and shielding it from saltwater with only a flimsy drybag.
My Hobie i12s... sailboat in a suitcase! Look for it in THIS