this is what will happen.
all of the johto pokémon will be in, (obviously)
all kanto pokémon will be in, with the exception of:
starters
Kabuto, Omanyte, and their evolution families,
Legendary birds.
(mewtwo has been confirmed to be in, so we don't have to worry about that.)
many of the hoenn pokémon will begin to appear after getting the national pokédex in swarms,new areas, and possibly pokéradar.
the number of sinnoh pokémon: 0 (with the exception of some events) all of these pokémon can be traded from D/P/Pt
i know this because this is what happened in firered and leafgreen. the johto pokémon started appearing on the sevii islands after getting the national pokédex. no third gen pokémon were in, because you could trade for them with R/S/E.