The second they revealed the Mega concept I saw this as a smart way of adding new designs to the series without having to constantly inflate the dex into absurd territory every gen. I feel like this will become a trend from now on, adding just a few new Pokemon to the dex with each new gen, along with some new designs for existing Pokemon via Megas.
In a way, Mega's help future proof the series. I don't think Gamefreak wants to get to the point to where they'll literally be dealing with a Pokedex count exceeding the quadruple digits. I think they're starting to realize how impractacle its going to eventually become, so they're putting a bit more pressure on the breaks to try and slow the series from just careening off track. Alternate Formes was their first method of trying to curb the inflation of the series, by allowing them to add new designs without having to actually create new Pokemon. The problem is that with Formes, there is no universal method of presenting the mechanic, as each Forme is obtained and functions differently from another species's alternate formes. However, with Mega's they created a simple, universal method to create new designs for any Pokemon that is immediately intuitive to anyone who's already familiar with the concept. It's actually really smart on their part, and gives them all the tools they need to add as many new designs to the series as they want in the future, without simply tacking on +100 more to the total Pokemon count with a new generation.
Im not saying that they're going to get to the point where they release a new gen without adding any new Pokemon to the series (though really, that wouldn't be a bad thing), but I think that now there's less of a chance that they'll feel that they HAVE to add tons of new creatures to justify a new game. Perhaps then they'll feel more comfortable branching out and innovating the series in other ways, rather than relying on the crutch of new Pokemon to sell the games.