Except that it was reflecting the Red and Green/Blue remakes of Fire Red and Leaf Green down to the character design of PT which was technically third gen. Chances are they were chosen because of that and because Red/Pokemon Trainer was also a highly requested character in the Melee poll with most of the Brawl newcomers (except Lucario, Ike, Olimar, ROB, and ZSS for obvious reasons) coming from that source.
Pocket Monsters series
(1) Mewtwo: 35
(2) Mew: 24
(3) Satoshi (main character): 18
(4) someone from Pokemon: 12
(5) Lugia: 11
(6) Nyarth: 8
(Meowth)
(7) Raichu: 7
(8) Maril: 5
(8) Fushigidane: 5
(Bulbasaur)
(8) Togepi: 5
Keep in mind that Mewtwo was considered for the original but was left out due to time constraints.
Also, Sakurai has shown that he does, in fact, care about relevance.
http://www.nintendo.co.jp/n01/n64/software/nus_p_nalj/smash/PostReturn007.html
On the post labeled YH, a fan asks about Princess Daisy and he subsequently turns down the idea because she didn't play any important roles as of late. Sakurai does make exceptions for retro franchises but, that's the thing, Pokemon is hardly retro and changes dramatically from generation to generation. Pikachu is the franchise mascot and Jigglypuff has been in all three games so the fact that the both began in the first generation is irrelevant.
All this being said, PT could stay but I'm not holding my breath and wouldn't be surprised if he left.