As much as people want to believe slots don't exist, developing characters takes time. So when time isn't put into a character you don't care for, there's a chance another character you do care for will get that time.
It has nothing to do with wanting to screw someone over, it's just that they can't put every character that everyone wants in.
Okay, so even if "slots" exist (and I'm not convinced), I think it's a safe bet that at this point, most if not all of us have at least one or two characters we're really happy about being in. We've all been pleased to some extent. What's with the mentality that "EVERY character must make me happy and fuck everyone else?" I don't personally care about Lucario, or Pikmin & Olimar, or Villager, or a couple of other characters. But that doesn't mean I view them as "wasted slots" because I recognize that (a) these characters are important to other people and (b) they're important to Nintendo's history/brand, thus they're not "wasted" just because they personally don't appeal to me.
My thought process is to have characters that are actually relevant at the time the game comes out, important to their franchises or to Nintendo's history. Lucario doesn't really fit any of those added on to the fact that I personally don't care for him and would rather have a more meaningful pokemon representative who could provide a newer more unique experience.
The same goes for Toon Link who should have had his own unique items and not the recycled boomerang, bomb, etc. And Wolf and Falco as well. I'm not going to get into a clone debate in this thread, but my point of view is that.
Just like there are fans of those characters there are people who don't like them and wouldn't mind seeing them either replaced by new ones or completely reworked.
I actually agree with you about Toon Link. I'm glad he's in at all, but he should have had his own move set from The Wind Waker/Phantom Hourglass/Spirit Tracks. I also agree that this is not the time to get into a clone debate.
I do disagree with you about Lucario, though. He had his own entire character arc in Pokémon X and Y, making him incredibly relevant and timely both to Pokémon and Nintendo. It's almost a given that Mega Lucario will be implemented into his move set in Smash 4 (Final Smash?), meaning that there really is no way you can argue that Lucario isn't relevant right now. He just is, and I don't think there's any reason his return threatents Mewtwo's return either.
More than that, though, you must have at least one or two characters you're personally really happy about in Smash, right? Then be happy about them. Why not do that instead of actively hoping for other characters to be cut (and, by extension, their fans to be disappointed, even if you don't actively want that)?
Well, it's cause I don't much care about other fans of characters. As a gamer, not a game-maker, I have the luxury of only caring about my personal experience with the game! And Snake being there bugs me. I'd be happier if he were out. I can stomach him as a one time "oh he he it's Snake" novelty, but he does not need to be a regular. He can come and go, thank you very much.
Then that's where we differ, I guess. I realize that Smash is a big deal to a lot of people and Nintendo fans, and I'd rather as many people as possible be pleased with it than just me. I've got my Mega Man, Rosalina, Toon Link, and Zelda... I've been spoiled already and am fucking over-the-moon hyped for Smash as a result, and it's a great feeling. I'd rather as many people have this feeling as possible than get five more newcomers/veterans that appeal only to me.