I don't think Punk's issue was that Punk/Jericho should have gone ahead of those matches, it's the idea that you are constantly giving Main Event status to part timers, to guys who 'aren't gonna be here Monday'. That is "bad for business" in the long run, and bad for the guys like Punk that ARE gonna be there every week, not only for their characters but also their wallets. Punk's main point I think wasn't "Me and Jericho should be themain event" it's "I'm the hottest thing you have going right now why am I taking a backseat to actors and MMA fighters?"
I think it's a little bit of both.
The majority PPVs that Punk was champ was main-evented by someone else. Cena was basically the uncrowned champion and it showed.
Survivor Series 2011 - CM Punk defeated Alberto Del Rio (c) by submission (Not Main Event)
TLC 2011 - CM Punk (c) defeated The Miz and Alberto Del Rio (with Ricardo Rodriguez) (Main Event, Cena not on Card)
RR 2012 - CM Punk (c) defeated Dolph Ziggler (Match before RR)
Elimination Chamber 2012 - CM Punk (c) defeated The Miz, Chris Jericho, Kofi Kingston, Dolph Ziggler (with Vickie Guerrero) and R-Truth (2nd of 6)
WM 29 - CM Punk (c) defeated Chris Jericho by submission (Not Main Event)
Extreme Rules 2012 - CM Punk (c) defeated Chris Jericho (7th of 9)
Over the Limit 2012 - CM Punk (c) defeated Daniel Bryan (8th of 10)
No Way Out 2012 - CM Punk (c) defeated Daniel Bryan and Kane (8th of 10)
MitB 2012 - CM Punk (c) defeated Daniel Bryan (5th of 8)
Summerslam 2012 - CM Punk (c) defeated John Cena and Big Show (7th of 8)
NoC 2012 - CM Punk (c) (with Paul Heyman) vs. John Cena ended in a draw (Main Event)
HiaC 2012 - CM Punk (c) defeated Ryback (Main Event, Cena not on Card)
Survivor Series 2012 - CM Punk (c) (with Paul Heyman) defeated John Cena and Ryback (Main Event)
TLC 2012 - CM Punk injured.
RR 2012 - The Rock defeated CM Punk (c) (with Paul Heyman) (Main Event)
Maybe one or two legit main events in the year + he had the belt.