There is a possibility that HM Whirpool will make a return, or it will be available by a Move Tutor in the game. However, I would expect it to make a return, or else the Whirl Islands wouldn't have much of a meaning if the player isn't able to experience the Whirl Pools that were once there in the originals.
To tell you the truth, I was disappointed at the fact that GSC didn't take good use of the Johto Pokémon they had at the time. I felt as though more could have been done. As much as the return of nostalgia is pretty nice, if the Johto Gyms [as well as the Kanto Gyms included] are revamped with certain new Pokémon, more so including more of the Johto species, then I wouldn't be bothered by it. There are some pretty decent Johto types who can make a well set for some of the Gym Leaders. Seeing as the Gyms itself have received a new look in the remakes, then I wouldn't be surprised to see some difference in the leaders that rest within them.
At least, if not a change in rosters, then a raise in level. I would later on expect a rematch to be called like in Emerald where the Gyms as well as Elites would raise in level and have a slight alteration in Pokémon. However, like you stated, there are some nice Pokémon options, such as Mistreavous for Morty. And like I stated, if a rematch were to happen, then he would later challenge us with Mismagius. Nice idea though, and it'll only be a matter of time before information on the gyms as well as the rest of the game is fully laid out on the table.