Toad - I don't think it really is an issue. If nothing else can use another item. Or heck, keep her Toad special and have a playable Toad still. The game isn't supposed to be logical. Plus I could think of some funny snapshots if that were the case...
Roy - Oh boy, I knew this would be controversial. Regardless of how people feel he is the most likely candidate, the fact he was in Smash Bros sets him apart from every other character. Because of that he will always be a popular character and familiar face. Like I said, popularity is popularity, it doesn't matter where you get it from. The only real scenario apart from Roy is we don't get another Fire Emblem character. Those are the two likely options.
Mewtwo - Again, I'll pose the question. Who determines that it is unlikely we won't have six Pokémon slots? It certainly isn't because Pokémon isn't large enough.
I dislike Lucario in both the Pokémon series and Smash Bros, but honestly there is no reason he should have to leave. He is still popular and has his fans. Pikachu and Pokémon Trainer sure aren't going anywhere, nor is Jigglypuff likely to go anywhere. If anything is truly unwanted it is a 5th Generation character!
But honestly there is nothing inherently wrong if Pokémon has six slots. Just like if Star Fox hase 4, or Earthbound has 3, or Metroid has 3, or any series has more then they are deemed too. It is not about series, it is about characters.
- I just feel that Sakurai may not put Toad in because of being neutral B Peach move and that Sakurai may not notice the move set potential in him. Then again, this is going into Sakurai's logic, which won't get us anywhere.
- There's also the fact that he was cut in the first place, hurting his chances considerably already. Also note that as you said, we may not even get a new Fire Emblem character and I have my doubts about us getting a new one this time around, plus he has a lot of competition if a new slot were to open up.
- To answer your question, it is Game Freak and Sakurai that decides if we get six slots for not and since I'd like to not be unrealistic, I don't expect six slots to happen. I would love for us to have Mewtwo, Lucario, and Zoroark/Victini/Genesect/Deoxys since I think the franchise is worthy of six slots, but I'm worried we may not even get five in SSB4.
Personally, I don't care who gets the fifth slot (I think the 5th gen will take the fourth one regardless) whenever that is Mewtwo, Lucario, Meowth, or Deoxys. Heck, they could have Scrafty in there and I wouldn't care as long as he played well. However, my bias prefers Mewtwo over Lucario. Still, you do have a point and I do think that Lucario should stay if nothing else as I think the Brawl roster + 5th gen rep would have me content.
However, you do have a point in which a 5th gen rep is the most "unwanted". As we all know, it is a sure bet that we are getting it so not everyone looks forward to it. This especially applies to Zoroark due to similar body structure, so the "hype" for him is more of "He's getting in." then "I want this character!". The fact that people put him on the roster merely due to expecting him turns me off big time and why I don't consider him the best choice we have. I think Arcadenik said something in regards to it. If someone can find the quote, I would appreciate it.
That said, I don't consider Victini to be just "expected", the supporters for it actually want him in SSB4. Having seen people on here and GameFAQs, I would say that if you take out all the people who just say "I support this Pokemon" and only include those who take the time to defend said Pokemon's inclusion, Victini is by far the most supported. What I want to see from Zoroark supporter is for them to have to literally actively defend his chances of being playable. Until that day comes when Zoroark supporters have to do that, I really don't see why people support him other then the general opinion that he's likely.