Ya know, this is actually a good question.
gen 1 and 2 remakes where rather simple, what with only having two mons for their titles they didnt really need to consider the third(suicune is of course the third in gen 2's case but its not part of the trio so fuck it)
As for gen 3 though, we now have trios which would make leaving it out rather odd. I seriously wonder what theyre going to do for it. Giving it alpha and omeag forms is a nice cop out but who knows
And then theres gen 4 with giratina. How will they go about it? Will both its forms have megas? Will it simply have a mega for alternate form since origin requires an item anyways?
And then of course gen 5 remakes
I cant fathom what theyll do with this one. Will they remake bw or bw2? will kyurem forms get the megas but not reshiram or zekrom? So much speculation to be had