It's all about money, heel Cena = less money; and that is not a good thing for the WWE right now with the recent cuts they have had to make. In addition to the money thing, both shows are too laden with top tier heels with Jericho, Orton, JBL, Edge, Show, and Koslov.
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I don't think that merchandising has much to with it. If being a heel affected your merchandise sales, then no-one would ever agree to be a heel (how much money do Edge and Randy Orton miss out on then, if they don't sell as many T-shirts). Besides, I see a few fans wearing "Rated-R Superstar" T-shirts on "Smackdown" every week, and Triple H T-shirts were popular when Triple H was a heel.
Also, the biggest example- Do you know what the biggest selling merchandise of any act in professional wrestling history was - The NWO!!!! Not Austin 3:16, not "Hulkamania" T-shirts, but "nWo"- a heel faction.
A heel act can sell merchandise if they are cool. Edge is considered cool, so he sells. Same with Triple H when he was heel, and the nWo . They were "cool" heels, so were still cheered, and thus people wanted to be "cool" like them.
You know what I bet. I bet that if John Cena went heel, he would still sell, because the fans may start to actually cheer for him. One of his major faults is that he comes across "too polite, too nice". Maybe a harder, more intense "heelish" darker Cena, would appeal more, not less. Kids would still want his shirts, because he would be "cooler" (in these days, wrestling fans consider "bad" as "cool"). Also, older wrestling fans would buy, because they would consider Cena cool, like nWo was cool.
You look at Cena when he was a heel in 2003. He was getting cheered so much, they turned him face. Heels are "cooler" so I think keeping him face because it may hurt his "marketability" is fallacy.