It's also coming out on the 3DS, in case you didn't already know.

No, because it's for but [U] and [3DS]

You must have never played Melee, Falco was a clone of Fox. Just like Roy and Marth, Pikachu and Pichu, Link and Young Link, and Mario and Dr. Mario.

Also Roy was planned for Brawl, files were found in the game for him. Also Marth's normal special move's motion gives the idea that it was changed so Roy could keep the old one. While that isn't confirmed, it would make sense why it had changed.

No, I clearly remember them having different moves. The majority of their moveset was identical, but there was a big enough change for them to have separate tiers.

Thats because of different stat parameters, and falco's moves having different knockback trajectories than Fox. Also because Falco's blaster NSpecial has hitstun where Fox's does not, Falco's reflector sends opponents upwards where Fox's does not. There are other things to consider when deciding tier placement.

Okay, so I'm trying to make a realistic SSB4 fan roster.

I'm almost done with the Mario section, but I can't decide between Bowser Jr. or Paper Mario.

Which one, eh?

Exactly. To me Falco and Fox are like Captain Falcon and Ganondorf.

I personally think Browser Jr. has a really good chance of being in and Paper Mario not so much.

Ehh, I suppose I'll just leave that spot blank for now.

Considering some of the reasoning I've heard for Paper Mario getting in.

Statistic differences doesn't mean a different moveset. Falco was a clone in Melee and was changed the in Brawl.
My point is that the same could have happened for Roy.

@Adam.
At this point Waluigi actually is better than both of them, since he's actually a really wanted character for Smash from the States and Japan.
Otherwise stick with Paper Mario because Jr. has been missing a lot of screen time as of late. He wasn't even in NSMB2, that's really the only main Mario franchise he appears in these days. ...But he might be in NSMBU.

nsmb2 was the first main series or sports mario game in almost 10 years that bowser jr wasn't in
he's not missing screen time

But Paper Mario and Waluigi have a better chance because they were released another generation before Bowser Jr. was, and even then, I don't really see Bowser Jr. as a really popular character. Waluigi has appeared in almost every spinoff since his debut in Mario Tennis, and Paper Mario has his own francise. Bowser Jr. just isn't special enough to be a Super Smash Brothers character.

Bowser Jr. shows up in almost spinoff titles, but also virtually every main title as well, often as a main character/the primary villain.

Waluigi has never been involved in a single plot driven, non-spinoff game, let alone as a main character. Waluigi only shows up in spinoff titles. He's never had any character development (Bowser Jr. has), and his personality is completely flat and dull. He was only created in the first place because they wanted Wario to have a doubles partner. In what way is he more special, exactly?

Also, might want to check this out before you pull out popularity arguments. It's well sourced. Waluigi is easily the most universally disliked Mario character.

waluigi is less special than literally any other video game character

Should I put in both Bowser Jr. and Paper Mario?

I could just put Paper Mario in another row to represent his own series...