WWE Championship matches and World Heavyweight Championship matches should always be the main event, unless there are special circumstances. They should do what they used to do, which is alternate which belt gets to main event, based on the stakes, stipulations, or star power of the performers in the match. Now it's just WHC comes before the WWE Championship. Always. Which I don't have a problem with because the WWE title IS the bigger world title of the two, so if they feel like one HAS to go over the other all the time, they're making the right choice as to which one it is. However I would alternate, it's not the way I would book.
There are special exceptions that can be made. The Rock vs John Cena main eventing is the right decision. Brock Lesnar vs John Cena main eventing is the right decision. Shawn Michaels' retirement match is the right decision. I don't have a problem with the Streak ever going last, at least not at this point. If they make a HUGE signing for WrestleMania, like Sting, that should go on last, by all means. If Stone Cold returns to wrestle, yes, you book that last. You put the Royal Rumble on last, it's tradition.
Beyond things like that, you put the title on last, dammit. John Cena vs John Laurinaitis and a MITB ladder match are NOT PPV main event worthy. Comedy fuckery, and a #1 contenders match overshadowing the title the #1 contenders match is FOR is complete nonsense (The Rumble is exempt, it's a special match). They can still promote John Cena as the #1 guy in the company, and he'll get the biggest attention going into the PPV, but there's no harm done to him by not putting him on last. The title is an accomplishment, most John Cena matches are not for anything specific, beyond a ridiculous firing angle that no one cares about, or they're #1 contender matches to the title it's being put ahead of, which is unacceptable and only hurts the title, whereas it wouldn't hurt Cena's standing to be where the title is.