It isn't really about Cena.
It is about the garbage heap of wrestlers he left behind him.
1. Build up strong wrestler
2. Go up against Cena
3. Short dancing gimmick and gooooone.
The actual issue was never Cena booked strong as a Top Guy. That's been wrestling, everywhere, since time immemorial (for a recent example - see Okada's run at the top of NJPW or for instance, Misawa's run in AJPW during the 90's).
The issue was, the WWE forgot how to book people after they lose to the Top Face. They used to actually be able to do this - see the careers of tons of people who got over in the 80's WWF, lost to Hogan just as clean as people jobbed to Cena, then were over enough to get giant contracts w/ WCW down the line.
The other issue was, the WWE learned the wrong lesson from The Rock. The Rock taught them the wrong lesson that you can have your upper midcard and top guys go 50/50 with each other, because The Rock could do. It turns out, the only people who can actually job all the time and stay massive stars are two of the most charismatic human beings on the planet - Rock & Flair.
As far as why Cena was the top guy for a decade plus - because there was no other option?
Now, I know the comeback is going to be "what about Punk?"
Punk was never going to be The Guy, because he was never going to do the things The Guy needed to do.
CM Punk was never going to learn Mandarin.
CM Punk was never going to wrestle a show in Phoenix, then hop on a 1 AM red eye to New York so he can do a five minute spot
on Good Morning America, then hop on another plan to Dallas to do local promos for the next RAW in three weeks in that town, and do that week after week.
CM Punk was never going to be the perfect company guy, that sublimated his indemnity to the WWE corporate PR team.
Plus, more importantly, the Cena Era worked. As much as smart fans hated a lot of it, the truth is - the WWE post-Attitude Era to the rise of Cena & Batista was in a ratings, PR, and house show attendance tailspin. Not only did the initial Cena & Batista programs increase ratings and house show attendance, having Cena as the guy allowed the WWE to push through the Guerrero/Benoit tragedies, and allow the company to turn from the racy product aimed at trailer trash people and teenage guys that got no sponsor money and had no positive mainstream attention to a company that could do deals w/ the biggest companies in the world and be involved in massive TV deal wars.
Remember, during the initial RAW move to Spike, and USA didn't really fight for it. So, they had to take less money from Spike than they expected. The only way WWE ratings could've gone even lower during the 2005-2015 era was if there was no insanely charismatic top guy like Cena to push as your top star.
I'd also point out that the moment the WWE's steady ratings decline went into overdrive and actually started falling faster than overall TV ratings all happened immediately post-WM XXXI and can be pointed to three main factors -
1.) The permance of three hour RAW's
2.) Rollins not being a true Top Guy, no matter how much Uncle Paul wants otherwise.
3.) Cena going from a Top Guy to a midcard act w/ the US Title. Yes, smart fans loved Cena going 50/50 w/ random midcarders, but your casual fan was likely turned off by their hero going from conquering badass who won all the time to having trouble w/ random guys.
I'm not saying all of the booking during the Cena Era was good. Far from that. A lot of it is terrible.
What I'm saying is John Cena being booked like every Top Guy since Bruno & Lou Thesz was not the main issue.
