Conspiracy theory time!
Villager and Wii Fit Trainer were partially chosen for the E3 reveals to save the more thrilling trailer reveals for later, hence Villager's being grouped into the main trailer and the WFT's being a good deal shorter than Mega Man's more traditional hype-inducing one.
By only showing off Mega Man, the most popular newcomer, Sakurai both gets the hype train chugging and distributes other 'big names' over the rest of the game's development time. And since even the unorthodox Smash characters can get fans excited, there's nothing to lose by getting these out of the way early, and arguably, a whole lot to gain.