No, he doesn't take up three slots. In fact, it seems like one of the big reasons the pokemon trainer is even incorporated is so that Charizard, Ivysaur and Squirtle take up one slot. Yes, it took time to make almost 3 complete characters, but they're all literally taking up the same character slot.
Actually I think it's the other way around. That Trainer Red was going to be playable and they chose to take the 3 starters of his gen and have them be his move-set.
But on to my point. Charizard, Ivysaur and Squirtle may only take up ONE "slot" but they are all complete characters that had to have the same (or around so) amount of time, effort, planing, balancing, coding etc as a character like MK/ Wario/ Pitt or Ike.
It's like this. . . .
Each character is like a 4 page essay (for example).
They have to make a 4 page essay and place it inside a folder for you to choose on the selection scene ( character slots ).
With pokemon trainer they had to not only make 3 of these 4 page essays but also make like 1 page for everything the trainer does ( things in Story mode/ tunts/ his command animations/ how ever he moves on moving stages/ victory dance maybe (he might be in them).) plus other things.
Now, with 13 pages of stuff, does putting it in one folder make any difference? Does it give them back all the time that was put into doing this? Does it = the same amount of time a effort put into only one character now?
Pokemon still has 4 Playable Characters as of now that we know of so does it matter if M2, Pichu and Jpuff come back and we only have 5 character slots on the sceen? That makes 7 characters for Pokemon just like how LoZ has 5 in melee (Link, Gannon, Y.Link, Zelda AND Sheik).
But I do think that we will get more new pokemon. . . what gens will they be from? Who will they be? How many will be added? IDK. . .