My roster, wrote out all my reasoning but my computer froze. So, I think theres a decent chance that Robin and Chrom could be switched ith one another, as well as Kalos for Kanto. Takamaru and Shulk are other characters I could see being included, if the roster was larger.
Seems pretty solid to me, just a few minor things.
I have to give you props having Tingle (and a Zelda newcomer overall).
The only changes I'd make is putting Snake back in (there is no reason at all for him to be cut), and adding one or two more newcomers to bring it up to 49 or 50. Personally, I'd have Takamaru and the Shulk.
EDIT: Also, no Kalos Trainer. The whole purpose of Trainer in Brawl was to showcase the actual character you play as, and to show the original starters, which are some of the most popular Pokémon even today.
If Sakurai wanted to make it a recency thing, he would have added Sinnoh Trainer in Brawl.
EDIT 2:
Let me put it this way.
With someone like Mario, he is Nintendo.
There's no other mix. You can't think of Mario without Nintendo.
With Layton, it's different.
It's not like he's an essential part of Nintendo.
He could go on without being one of their consoles.
But he DOESN'T go on with other consoles. He sticks with Nintendo all the way! That's why I think he is a Nintendo character at heart.
I can't say that I know what the exact technicalities of getting third party characters into Smash are (nor do I think anyone else here does), so I can't really argue with that.
As for that last part... Professor Layton is not owned by Nintendo, and therefore, even if he is almost exclusively on their systems, he is not a true Nintendo All-Star. Because he's not Nintendo.
However, this bit seems highly debatable and up to individual interpretation, so...
I know Layton isn't owned by Nintendo, since that's the basis of this whole discussion.
Just because he isn't on paper owned by Nintendo, he is still an all-star who is associated with no other big company than Nintendo. Therefore, a Nintendo All-Star.