They're trying to promote the Nintendo 3DS...with a Nintendo DS game? For all we know, Creatures Inc. could be developing Pokédex 3D Pro (as they did Pokédex 3D) and we don't know who is developing Pokémon AR Searcher.You seem to be ignoring the fact that Game Freak are trying to promote the 3DS. Not completing the regional Pokédex wouldn't hurt anyone, just as it wasn't an issue for Manaphy to be in the middle of the updated Sinnoh Pokédex. We could still see Manaphy because then seeing all the Pokémon was a requirement. For all we know, Professor Burnett might appear in B2W2 to tell the player about the Formes, which would at least add their data as having been seen.Besides, I think it would be an even bigger tease to have three Pokémon in the middle of the Pokédex that are unable to be caught in the game unless you pay 15,000yen to purchase a Nintendo 3DS (if you don't already have one), then another 150yen to buy the AR app, THEN have the luck to encounter one of the trio in the game (I highly doubt they'll be common).
As for Manaphy, GameFreak were just lazy in that they just dumped all the added Pokémon at the end of the pre-existing Sinnoh Pokédex regardless of where they appeared in the game. This time we've had a complete re-order.