What I think will happen is the remake will be considered canon(unlike TOR since it's before the disney era) and they might remake TSL as well, so they might decide to take a new route and make a entirely new 3rd game.
From my understanding everything before disney is legends(TOR included), the remake is after the disney deal,so new old republic canon it is.
Valid point... I did not like SWTOR either, though I don't think Aspyr will try to assume what happend in SWTOR, in fact EA is not even invovled in this project ... it's all lucas,sony and aspyr, so If lucas gives green light to aspyr( which I think it will, because every material released post Disney deal, is canon)to head a new canon, they could take the series in entirely new direction after the remakes and disregard TOR ever existed.