The Good: Cena is the company man to end all company men. Even today, after an insanely long run with the company, everything dude does is for the good of WWE in some way. Vince probably wishes he could clone him, or at least attach his sense of loyalty to some of these new cats who are about themselves first. WWE has been able to make a lot of strides getting back into the mainstream and opening new media avenues for talent, and a lot of that has been on the back of Cena.
He has improved in the ring in recent years to acculmate to the current popular styles of wrestling. I bet if you made a list of all his best matches, most if not all would be in the back half of his career. He's also dedicated himself to putting more guys over in recent years as he transitions out of wrestling full time.
Despite the fact that his character is pretty corny (I'll get to that), you can't deny that he's great on the mic. Again, this is also something he's gotten better at with time. (Also helps the crowds have softened on him a bit in recent years)
Dude has been a consistent draw and merch seller for over a decade, which is probably the most important factor for a pro wrestler. As has already been noted in other posts, he's made the company an insane amount of money.
The Bad: John Cena's time as the top guy is also a time where WWE has seen a massive drop off in TV ratings, live audience, and PPV buys (now Network subs). Now, I'm not going to say that is entirely Cena's fault; there's a ton of factors that drove away the audience. But, loathe as the Cenation might be to admit it, John was one of those factors. A lot of people decided they didn't like John's character nor seeing him constantly go over and be the center of everything, so they tuned out.
Again, not saying that's all on him. But I think if we're going to fairly access Cena, we gotta look all the effects he had on business and the full context of his time in the company. And the fact is, a lot of people didn't - and still don't - like what he was selling.
Remember how I mentioned being corny? Yeah, "John Cena" the character is pretty awful. When he's not being a creepily patriotic ripoff of Superman, he's a childish bully who goes out of his way to embarrass opponents. His promos, while good, often ignore half the things the other guy says. Example: in a segment with AJ, he said wrestling is just a job to Styles while he (Cena) does it because he loves it. This was not two minutes after AJ said he would wrestle in high school gyms if he had to because he loves doing it so much. He also has some crazy plot armor where the company is always protecting him (a fact that John Cena the person seems kind of blind to).
As a performer, while again the back half of his career has been better, I still say he doesn't quite match up to other guys. He's not as good in the ring as, say, Bret or Benoit. Not as good on the mic as The Rock. He's still quite good, but as others have said, I think he really benefitted from coming up at a time where most of the locker room was really mediocre or even just flat out shyt.
Overall, while he's not my cup of tea, I think one would be hardpressed to justify ranking anywhere below one of the greats in WWE history. The good he's done for the company and the fact that he's had such a long run at the top outweigh the bad points for me. I will say though, he's definitely going to leave the company a little worse off than he found it. Vince put all his eggs into the Cena basket for so long, and we're just starting to see the aftermath of that in how they can't seem to figure out how to create new stars.
Though I wonder how much of it is "they can't" and how much is "they can, but they want someone who is going to be just like Cena."