To be fair, the WWF was in bad shape when he was the top dog. 1996 is one of the company's worst years in the last three decades.
It also didn't help him that he was given a vanilla baby face character that didn't suit him well and he was competing against the nWo angle when it was the biggest thing in wrestling.
If you swap prime Cena with Michaels in 1996, I can't imagine he draws much if any better (he's using that "Thug" character and it hasn't gotten stale yet).
I think people may be forgetting how divisive Cena was during the "Super Cena days;" it wasn't just ICW members that couldn't stand him; large sections of the crowd would cheer the guy when he was the top baby face in the WWE. The meme was, "all the women and children love him; the men hate him."
Another knock against him from a reception standpoint is that he was a face the vast majority if not the entirety of his stint as a main eventer. Could he have been an effective heel beyond 2003? We can't say for sure. There was speculation he might finally turn heel during the Nexus angle, but of course he never did.
You make some good points, I won't argue that.
Part of the problem was that HBK just wasn't much of a draw as a main event headliner
I pulled this up from another fans research
And still the WWE machine try to manipulate the fans to turn him goat.
Royal Rumble PPV buyrates:
(1.10) - Bret Hart vs. Taker - RR 96
(1.00) - Diesel vs. Bret Hart - RR 95
(0.90) - Yokozuna vs. Taker - RR 94
(0.70) - HBK vs. Sid - RR 97
WrestleMania PPV buyrates:
(1.68 grossing $5.2 million) - Bret Hart vs. Yokozuna - WM 94
(1.40 grossing $5.1 million) - Diesel vs. HBK - WM 95
(1.20 grossing $4.0 million) - HBK vs. Bret Hart - WM 96
(0.77 grossing $2.5 million) - Taker vs. Sid - WM 97
King of the Ring PPV buyrates:
(0.85) - Piper vs. Lawler - KOTR 94
(0.65 ) - Diesel/Bigelow vs. Sid/Tatanka - KOTR 95
(0.60) - HBK vs. Bulldog - KOTR 96
(0.50) - Taker vs. Farooq - KOTR 97
SummerSlam PPV buyrates:
(1.30) - Taker vs. Taker - SS 94
(0.90) - Diesel vs. Mabel - SS 95
(0.80) - Bret Hart vs. Taker - SS 97
(0.58) - HBK vs. Vader - SS 96
Survivor Series PPV buyrate:
(0.90) - Taker vs. Yokozuna - SS 94
(0.89) - Bret Hart vs. HBK - SS 97
(0.58) - HBK vs. Sid - SS 96
(0.57) - Diesel vs. Bret Hart - SS 95
In Your House PPV buyrates:
(0.83) - Diesel vs. Sid - IYH 1 [14 May 95]
(0.75) - Diesel vs. Bret Hart - IYH 6 [18 Feb 96]
(0.70) - Diesel vs. Sid - IYH 2 [23 July 95]
(0.70) - Diesel/HBK vs. Yokozuna/Bulldog - IYH 3 [24 Sept 95]
(0.65) - Diesel vs. HBK - IYH 7 [28 April 96]
(0.60) - HBK vs. Taker - IYH 18 [5 Oct 97]
(0.59) - Hart Foundation vs. Team USA - IYH 16 [6 July 97]
(0.57) - Austin vs. Taker - IYH 15 [11 May 97]
(0.50) - Bret Hart vs Taker vs Austin vs Vader - IYH 13 [16 Feb 97]
(0.50) - Bret Hart vs. Austin - IYH 14 [20 April 97]
(0.48) - HBK vs. Mankind - IYH 10 [22 Sept 96]
(0.45) - HBK vs. Bulldog - IYH 8 [26 & 28 May 96]
(0.45) - HBK vs. Taker - IYH 17 [7 Sept 97]
(0.44) - HBK vs. Shamrock - IYH 19 [7 Dec 97]
(0.40) - Diesel vs. Bulldog - IYH 4 [22 Oct 95]
(0.40) - Taker vs. Mankind - IYH 11 [20 Oct 96]
(0.37) - Vader/Owen/Bulldog vs. HBK/AJ/Sid - IYH 9 [21 July 96]
(0.35) - Bret Hart vs. Sid - IYH 12 [15 Dec 96]
(0.33) - Bret Hart vs. Bulldog - IYH 5 [17 Dec 95]
Diesel/HBK comparison:
(1.00) RR 95 - (0.70) RR 97 (bigger draw = Diesel)
(1.40) WM 95 - (1.20) WM 96 (bigger draw = Diesel)
(0.83) IYH May 95 - (0.45) IYH May 96 (bigger draw = Diesel)
(0.65) KOTR 95 - (0.60) KOTR 96 (bigger draw = Diesel)
(0.70) IYH July 95 - (0.37) IYH July 96 (bigger draw = Diesel)
(0.90) SS 95 - (0.58) SS 96 (bigger draw = Diesel)
(0.70) IYH Sept 95 - (0.48) IYH Sept 96 (bigger draw = Diesel)
Vanilla baby face or not, he just didn't really draw.
John Cena was certainly divisive, but he was nowhere near as destructive as Sean was in his day. He did a great job of reinventing himself and reforming himself after his conversion, but people forget how outright hated he was in the WWE locker room, to the point that Undertaker threatened him with a beating to death.
Also people tend to forget that at its height of dominance people started to get pretty sick of the kliq and then later De-Generation X even though HHH takes a lot of heat for that.
Cena drew because of his face character, he appealed to their main demographic at the time but the people that really hated him were the smarks who wanted anyone pushed but him. But his appeal to kids and the general non smark market generated a ton of money and merchandising cash.
In comparison of in ring skills, Sean Michaels is just far better. But as someone pointed out, I can't remember a really terrible John Cena match, but I can remember a lot of really safe John Cena matches, in that way he was similar to the Rock.
Also Cena's image just blows away Sean's, the charitable stuff and his ability to transcend out of Wrestling is very Rock like and only two performers have pulled them off and that's the Rock and Cena, unless your into low budget Christian movies.