I think the struggles are much simpler than people realize. About 2/3 of the way through the season, teams realized that by trapping every Auburn ball screen they could almost entirely eliminate the Kessler/Cardwell pick-and-role. At its peak, this was accounting for something like 30 points a game and now that its production has vanished Auburn is seriously struggling to find points elsewhere.
Of course, if you trap everything and extend your defense up, there will be open lanes for cutters everywhere, provided that your guards can find these cutters. I suspect (although I don't know, I'm no analyst) that Wendell is simply too short to take advantage of this. Additionally, when a defender rotates down to contest an inside shot, there will always be someone WIDE open on the perimeter, we just, as anyone with eyes will tell you, can't make those shots. And we never will.
I took a quick glance back at the box scores during the big winning streak, and against everyone except pretty much Kentucky they shot under or near 30% from three. If they shot a consistent 35% (Which is pretty much the mean for a college basketball team) this team would be essentially unbeatable. As it is, we have to play absolutely horrendous basketball to even lose close. If they clean up some of the truly dumb offensive plays (I can't count how many times KD has ignored a wide open player under the basket in order to drive directly into two guys and miss) this team will roll into the sweet 16, after that its a crapshoot.
In all, this team reminds me of the Duke teams of the last 7 or 8 years: overwhelmingly talented, but inexperienced and fatally flawed. I think we suffer the same fate as them - 2nd or 3rd round upset.