It is a combination of things, including some of the things (questions) you mentioned. But some of the major reasons include:
1) People overestimate the talent and abilities of the players we have. While we have had (and still have) some good players and decent shooters, we lack players with the talent to create 1-on-1 and consistently beat their defenders off the dribble when guarder closely. For example, Nunn has a quick release and gets great elevation on his jump shot. But unless he has some space he can't consistently take his man off the dribble. Hill will back his player down and use his fade away and step back moves, but he is not great at creating and driving to the basket when closely guarded.
2) We have major, MAJOR gaps at key positions. No real PG who can create and put pressure on defenses. No post/inside play. Even with Thorne totally healthy, people forget that he only averaged 22-23 minutes per game. Thorne was not a player who could consistently give you 30+ mins of inside play. And as much as I really like Finke as stretch PF (and believe he will develop into an excellent player in the B1G), he is not a C/post. I never bought into the mantra that we recruited a stretch PF and a C arrived on campus. We recruited a stretch PF and a stretch PF arrived on campus. And after a year, he is still a stretch PF.
3) So without quality PG and inside/post play, defenses just extend to the perimeter guarding closer. Add the fact that we do not have many player options who can create, it is a recipe for mediocre play.
Bottom line is that Groce's coaching leaves a lot to be desired. Without talent, and I mean highly ranked talent, he won't be consistently successful. If he gets talent, his coaching schemes will look better, despite his deficiencies. But without talent, he has no chance.