It's both the from the PG position + the Pierce/Green wing combination.
PG position = lack of a dribble penetration and playmaking
Pierce/Green = leads to too many isolation and post up (mainly mid post action) plays. Which when combined with two mid-to-high post big men makes the floor to compact. Not enough spacing. Very easy to defend against. Easy to show or double on help defense and recover to shooters who are nearby. Floor not stretched.
Both are situations that need to be addressed going into next season. Rondo is the easy fix at PG. A better backup PG is clearly necessary also. And then Pierce + Green need to be broken up. One needs to leave. There isn't enough minutes for both of them and they can't play well enough alongside one another given the makeup of the rest of the team.
I totally agree about the back up point guard situation. I know you've been sounding the trumpet for JJ Barea for a while now, and I think he'd be a great fit.
Looking at a lot of the successful teams out there, many of them have multiple ball handling guards (often, employing them together). Golden State has Curry and Jack, New York with Felton, Kidd, Prigioni, the Clippers with Paul, Billups, Crawford, and Bledsoe. Dallas' championship team often went with a multi-guard, multi-penetrators lineup, which was a big difference maker for them in those playoffs.
I never mistook Avery for a point guard, but I thought he'd be able to give us a little more in the penetration and shot creation department with Rondo down. That wasn't to be.
I sort of agree with your Green and Pierce point, as well. I'd just hate to see Paul Pierce go, and would rather keep him and have him play in a more limited backup role. On the other hand, if we can get some quality front court help in return for Green, then maybe that's worth thinking about. With more backcourt, ballhandling and penetration, that should help the Captain not have to carry the load so much.
One more run.