The best reason I can give for Cena being worse in the same position and role as Tanahashi is that in Cena's case he's not just in the main event, he is the focus of everything. Nothing on the card matters even remotely as much as and the next closest thing is the Taker match, but that's gone now too. At least in New Japan all the title matches are important, the midcard matters and even the undercard filler matches are not downplayed.
Just because Tanahashi is in the main event, doesn't do any of the other guys any real harm, there are many titles guys fight for that are almost on equal ground as then main title and their matches get focus and attention too. In WWE half of the matches matter and the other half are booked the week before Mania and go for ten minutes as commentary talks about Cena and how much he struggled to get the main event and how he must overcome whatever.
Granted, I don't speak Japanese, so maybe they do that too there. But somehow I doubt that.