I think Punk made a lot of great points about the problems inside WWE. Specifically:
1) Too much micromanagement and competing agendas among management.
2) Lack of any clear direction regarding booking.
3) Poor talent relations staff that is unknowledgeable about wrestling and also fail to actually represent the wrestler's concerns.
4) Too many writers and not enough wrestler input into promos/storylines.
5) Conflict between attempting to be a true 21st century corporation while still maintaining unprofessional traditional wrestling and family business-style practices.
6) Conflict of interest with doctors who are employed by the WWE.
7) Bad concussion policy.
Bad vacation policy.
9) Emphasis on former stars for PPV events when they don't necessarily still provide the best matches and usually have shoehorned-in storylines.
10) Lack of confidence in pushing new stars over old ones.
11) Prejudice against smaller-sized wrestlers (he didn't bring this up specifically but I'm throwing it in there).
12) Possibly making the wrong decision(s) with the implementation of WWE Network (to be continued).
13) Abiding too strictly to the PG-friendly era.
14) Promoting Cena so hard that it overshadows other stars on the roster.
15) El Torito.
OK, I made the last one up.