The 3-4 in general. Granted, BP knows it and should be able to tell if it works, but a scheme that takes your best defensive player off the field (Glover) and limits one of your better defensive lineman to grunt duty as a 3-4 end where his effectiveness is limited (Ellis), concerns me a bit. Not to mention that the team is counting heavily on two rookies (Ware and Spears) to not only adjust to the NFL but to a new scheme as well. James/Shanle are a huge question mark at ILB. NT depth behind Ferguson scares me. The other OLB spot (opposite a rookie who hasn't played it before) scares me. And it could be another rookie (Burnett). The 3-4 run defense with the current lineup scares me as well. It seems I am easily scared!
However, after all that, I have faith in BP and if he thinks he can get a competitive 3-4 on the field, by all means go for it. I just hope he doesn't sacrifice better overall talent on the field in favor of scheme.
FS really doesn't scare me as much. I think with Roy, Newman, Henry and Glenn, the team has enough talent in the secondary to cover up inexperience at FS. Reese is nothing special, but he is known as solid and intelligent, so I think the team is better off there this year.
So, in summary, I guess one OLB, one ILB and the removal of Glover from the field are my biggest concerns.