I tend to disagree. I concede, Palutena did have a group of supporters from the beginning (but then, so did most characters). Comparing her to the popularity of Ridley or Mewtwo is ludicrous to me, as I'm almost certain the only reason she comes up so much in conversation nowadays is because of the infamous Palutena leak, which is the only remotely convincing leak to date.
Think back to E3 2013. Everyone knew who Mega Man and Wii Fit Trainer were - Mega Man is a staple of videogaming in general, and Wii Fit was one of the most casual games in the Wii era. As for the Villager - he is essentially a generic avatar, so you can see why recognition for that character wouldn't be as important.
How does Palutena stack up to these, then? Well, she is a fairly obscure character. Kid Icarus is by far one of Nintendo's most popular franchises, and even then, Palutena is not as important to the franchise as Pit himself.
Just remember, the bubble that SmashBoards and the rest of the Smash community operates in is not representative of the entire audience for Smash Bros. In fact, you could say we are the minority. Outside of this bubble, I can imagine Palutena being barely ever spoken of.
TL;DR Palutena is not well-known enough to be shown at E3, like I said earlier.