Cute.
Well, unfortunately I can't speak for Fire Emblem games outside of the more recent ones like the Tellius series and Awakening, so I wouldn't be able to say how important those specific characters you mentioned are. But again, keep in mind, I'm not saying Lucina isn't important to her game, just that she's not important enough to make it into Smash. There's a difference, I think. Ike's multiple game appearances justify his inclusion into Smash, as well as his late appearance in Radiant Dawn. He's still the most important character from that saga of Fire Emblem.
As for that Mario comparison, it is completely invalid because you forgot about Luigi.
In all seriousness though, it's sort of hard to say what Sakurai would think in this sort of scenario. He might very well go for the more popular character if they are so close in importance. A few things I might want to point out though. One would be potential uniqueness. I know you've already said that you think that the only reason people support Robin is because of the "uniqueness is everything" idea (which isn't quite the case), but it does seem that Sakurai looks at how the character could be a unique fighter when considering characters. Robin definitely wins out in this category. His vast amount of skills he can gain in Awakening, as well as his default ability to use swords and magic simultaneously, gives him the most potential to be unique between him, Chrom and Lucina. There's also the issue of popularity. Lucina is definitely popular, no doubt about that. I believe she's the most popular female from Awakening based on that poll. However, Robin is right behind her. Both male and female Robin are pretty close, if not right behind, Chrom and Lucina in terms of popularity. So the difference in popularity isn't that huge, perhaps not huge enough to actually warrant Lucina's inclusion over the more important Robin (or Chrom for that matter, who's the most popular male from that game, but I'm more focused on Robin here). So, with that considered, I would say that the more important character(s) would be more likely to be included over the less important, although a bit more popular, character.
As for Red, I would say that the Pokemon Trainer themselves is not something that is heavily advertised. There's a bit more focus on the Pokemon themselves rather than the Trainer. Still, the Trainer is very important in the games, and his presence on the roster, as opposed to just Charizard alone, for example, indicates that a characters importance to the series/game overall does matter. Even if that character isn't the face of the game or the most marketed character of the game.