This is iffy. While I would love another Giratina-type scene in the remakes, I just don't see how it could be fit in. Rockets go after the mascot, which is version exclusive? i dunno.
However, they could include Eusine and have the beast catching quest available.
I don't want to see the same storyline as the originals.
If this were in the same vein as Suicune's "involvement" in Crystal's story, then I would have absolutely no arguments. However, a fair amount of this popularity is coming from nostalgia of one form or another, and I believe that adjusting the story specifically to fit one of the Legendaries would damage that.
Also, I must admit that it would be enjoyable to play a game once again where the Legendaries are not imperative to the plot.