Boosters would sag the wings on any toy plane, or any real plane for that matter, they're big and heavy. I don't think Yamato could have made them any lighter than they are and the wings are too thin to incorparate some sort of support system into them.
Missiles stay on fine on mine, they're just a little hard to click into place.
Once transformed to battroid, the upper legs can be pushed into the hips to make them more tight. Standing shouldn't be a problem after that.
The landing bay doors are fine on mine.
The shoulder design is, indeed, very complex and scary to transform.