Well by that logic all the fire emblem characters should replace the current reps ignoring the 9 previous games in the series and Lucas should be swapped for paula and ignore the other two games in the series. I get they are the most known/loved and they are the majority of pokemon reps, but it still doesn't make sense to disregard any other gen just because it wasn't there from day 1. (I am not saying what you say is wrong, I am just saying gens 2 through 6 shouldn't be counted out just yet.)
In Fire Emblems case; Marth, Roy and Ike have all represented Fire Emblem significantly in someway or another; Marth is the first lord, Roy was picked for individuality at the time(ironic since he became a clone) but his game was one of the best selling in Japan(see Chronobound's many talks for detail on Roy's impact on the series), Ike's games did really well in the west and I dare say Awakening will get one for saving the series from dying off.
But so far all these characters are main characters. They're all the protagonists of the games that shaped the series(even if Roy was a total gamble on Sakurai's part).
Same with Lucas being added instead of Paula. He is the protagonist, ergo he is the addition. I know it was popular and well recieved in Japan, but that's about as much as I can dabble in Mother.
Pokemon, however, doesn't have a protagonist Pokemon as such, and therefore seems to fall under different rules, at least judging from past games; Gen 1 getting more than the lions share of repping.
I dare say Lucario will be back. Pichu's also represented a generation. It's not out of the realm of possibility that Gen 5 or 6 get a newcomer too. I just can't call them all stars of Pokemon. They're just another face in 800 odd choices.
Of course, this is all redundant anyway since Gen 6 is getting reps even if it doesn't get a newcomer: Puff is part Fairy now, Mewtwo and/or Lucario will probably have their Mega Form, etc.
This all sounds a bit aggressive on my part, but I assure you I'm not trying to annoy you. I'm just pointing out that Pokemon 152 and onwards haven't shaped the franchise as much as the original 151. If Pokemon X and Y shape it outside of finally bringing 3D models to the games, I will happily welcome a gen 6 Pokemon.
That said;
MEOWTH FOR SMASH 4!