It's pretty clear to see that Punk was mishandled coming off of all the momentum he built leading into MITB in Chicago. I'm a huge Kevin Nash mark, don't get me wrong, but his inclusion was unnecessary and the whole text message angle involving Triple H was overly complicated and ultimately pointless. Also, the fact that they blew their load on the Punk/HHH match after like one month was a wasted opportunity.
After Money In The Bank, they did the angle where Vince was replaced as the head of the company by Triple H. Triple H then decided to have a tournament to crown a new WWE Champion. This idea was fine, but I think they should've stretched the tournament out a little more, maybe had 16 competitors in it, and held the finals at SummerSlam. CM Punk would continue to make off-TV appearances with his WWE Title, like what they did at Comic-Con, and could maybe post some videos on YouTube. Rumours would then be leaked online that he was going to show up at SummerSlam in the crowd. This would peak the interest of the audience as they would be wondering what Punk might do at the show. In the Information Age, it's very easy to keep someone highly relevant in the minds of fans without having them appear on TV, things like YouTube and social media can accomplish this wonderfully.
So this brings us to SummerSlam, where we have our tournament finals of John Cena vs. Rey Mysterio in a huge face vs. face match in the main event. CM Punk is in attendance, with his own WWE Title. John Cena wins the match against Rey, and is crowned the new WWE Champion. CM Punk then jumps the guardrail and decks him with his Title belt before getting taken down by security as the pay-per-view does a hard cut to black, ending the show (we don't see the typical end of the show logo or anything like that).
Leading up to Night of Champions, it is revealed that Triple H has managed to re-sign CM Punk, and Punk explains his motivation for coming back (so that he could affect change in the WWE, alter the status quo AKA John Cena on top, and be the "voice of the voiceless"). This leads to our main event at Night of Champions, WWE Champion John Cena vs. WWE Champion CM Punk. Night of Champions is much more fitting pay-per-view for this match. Of course, during this whole time we are seeing tension between CM Punk and Triple H and Punk continues to push the boundaries, saying some controversial things on the mic.
So, at Night of Champions, CM Punk wins, becoming the undisputed WWE Champion. We continue to see Punk play the anti-authority role, as tensions continue to mount between he and Triple H. The next pay-per-view is Hell In A Cell (fuck Vengeance, that PPV should never have even happened). John Cena challenges CM Punk to a re-match, inside the Cell. Punk accepts on the condition that if he wins, John Cena will never get another shot at the WWE Title as long as he's champion (you could also make the stipualtion that he'll never get a WWE Title shot at any time in the next year). This stipulation makes sense as Punk is trying to affect change, and he doesn't want Cena in the main event spot any more. Punk believes Cena's been in the title picture too long and it's time for something fresh and different. Cena accepts this condition, setting the stage for a huge Hell In A Cell Match, to conclude their rivalry.
In the promos leading up to Hell In A Cell you have Punk talking about the blood and weapon restrictions currently in place in the WWE, and say that he's throwing all of WWEs "PG policies" out the window come Hell In A Cell. This would make all the internet fans wet in their pants and would hype up the PPV immensely for the audience at large. For it to work though, Cena and Punk would legitimately have to be willing to break the no blood rule and get busted open in their Cell Match. This once again would make Punk seem "cutting edge" and "controversial" which is the whole point of his character.
Punk would of course win the Hell In A Cell Match, ending the feud with Cena. The problems between Punk and Triple H would then start to mount leading up to WrestleMania where Triple H would take matters into his own hands, and step into the ring against Punk. Their feud would have been building for months by then without any real physical interaction and it's the perfect match for Punk at WrestleMania. It's the authority vs. the anti-authority, with the future of the WWE in the balance. it's such a great clash of characters and both Punk and Triple H are great workers so they could deliver one hell of a WrestleMania match. Yes, this would mean undertaker would have to face somebody else, but it would be worth it as this would really help to establish a new star that could be a selling point for numerous WrestleManias down the road. If you HAD to have Taker/HHH you could do Punk/HHH at the Rumble perhaps, so it still has a lot of build up to it and its at a major PPV.
So yeah, that's more or less how I would've handled the whole situation to better capitalize on Punk's momentum and put him over as a bigger star. If you read through all of that, I appreciate it. What it comes down to at the end of the day, is that Punk was a guy who got extremely over as a face, extremely quickly. It took WWE by surprise and they didn't know how to best take advantage of the whole situation mainly because I don't think they really understood the appeal of CM Punk's character.