You're correct about the fact that Special sometimes uses entirely different personalities for the characters; this actually makes this merge somewhat passable. But either way, it's true that the Kris/Lyra thing is very debatable, and there has been a split of people believing either scenario. I personally consider them different characters; for reasons including their appearence, which is not very alike, their personality - I just can't imagine Kris being so happy-go-lucky, and not one her personas in other canons has been

-, and other references.
As for the Japanese fandom; it actually doesn't consider the remakes' characters seperate from the original ones. If anything, there has been some cross-appearences of Kris and Lyra or all four Johto kids, in Japanese fans' artworks from what I have seen.

Other than that, Lyra in Special would indeed cause some confusion, but I think that they could work it finely for her to fit in.
And Game Freak; well. We'll probably never know if they intended to have Lyra be a new character or Kris' reapperance. But with the fandom's reaction, I think that this matter is at least debatable. Hints, actually, lean through the first scenartio; there has been many official Kris artworks by Sugimori during, but not limited to the GSC saga. One would think that they wouldn't alter her appearence so drastically, especially since Ethan is mostly unchanged.
Again, these are all just personal opinions.