That doesn't negate my point at all, each generation since Gen 1 had always had a trio of its own (sometimes two such as with Sinnoh), that was something widely held to remain as the franchise went on, yet Gen 6 threw the tradition out and didn't make one of its own. Reusing the Birds doesn't change the fact that they didn't consider the "trio" archetype one worthwhile to keep going, and ultimately they didn't follow the previous examples of the other games and did something differently on its own. So if GF was willing to violate a tradition like that one (which is just as long held as the Mew one) and handle it differently, what says that the Mew archetype won't be (or wasn't)?
Adding to this, we also have to consider that they didn't see it as important enough to have in the initial games in the first place, so if it wasn't considered a necessity when they first started, it may very well not be considered a necessity now.
Not necessarily, the thing is the only connection that they currently have is through the movie, and the movies are allowed to make connections that aren't canon to the actual games. It could be more along the lines of Keldeo/Kyurem, Shaymin/Giratina or (to use a regular anime example) Meloetta/Forces of Nature then another Cresselia/Darkrai.
We just have to wait and see where the connection goes first before making any calls, it could be something, but nothing is saying otherwise for the time being.