Unfortunate to hear of all these horror stories. But at the same time, I feel those with the problems will be more vocal than those who are not having problems with their pano roofs.
As for the spare tire well being filled with water, I too, had that problem. It turned out that one of the drain tubes that feed into the rear wheelwheel was routed into the spare tire well. As these vehicles are not built in Germany, I can only imagine a sub-par workmanship, and for a drain tube to specifically be positioned in such a manner is not the result of car vibration, but lousy QC at the vehicle production plant. I corrected the routing, dabbed some silicone caulking, and it's been fine since.
I have mentioned in the other pano roof posts, the sunshade fix is a bit of a challenge, but doable. The first time around I guided the fabric incorrectly into the rails; that whole procedure took the better part of the day. The second time replacing the fabric, I think I cut it down to a third of the time.
I am glad to have a panoroof in my JSW, and it's one of the features I really praise.