We here at PNN noticed something interesting about current Raid Bosses when we were redesigning the Raid and Egg Charts recently: There is a lack of Johto-region Bosses. There are currently 25 Raid Bosses (27 with Articuno and Zapdos) available, with five of them being from Gen 2. This means that 18.5% of all of the Bosses are from Johto. Let's discuss.
There are many Pokémon (Scizor, Donphan, Houndoom, Kingdra, Espeon, etc.) from Johto that deserve to be Raid Bosses but are not. This seems even more strange when we consider that "useless" Pokémon, like Magikarp and Weezing, did become Bosses. So why is this? The most logical answer is Niantic doesn't want us to complete our Pokédex too quickly (especially after the addition of Rare Candy). Another is they don't want to add some of these Pokémon because of their unique evolutionary mechanic. This prolongs our interest in catching Pokémon and maintaining our streak patterns.
Regardless of Niantic's reasoning, we can expect new Raid Bosses with the addition of new Pokémon (Gen 3). Donphan, Ursaring, and Houndoom are the three most likely candidates for Johtonian Boss-ship. Some Kanto Pokémon, like Gyarados and Poliwrath, may also become Bosses. But what about Bosses from the Hoenn region?
Not including Legendaries, Croconaw, Bayleef, Quilava, and Tyranitar are the only Gen 2 Bosses to date. So, if Gen 3 follows the same pattern, the second-stage starters (Combusken, Marshtomp, and Grovyle) and the third-stage pseudo-Legendaries (Salamence and Metagross) would be available in Raids. It does seem extremely likely that Metagross and Salamence would become available later on, as Niantic cannot just "give out" extremely rare Pokémon.
Obviously, these are just PNN's predictions. We'll have to wait and see what Niantic actually does when they release Gen 3 (hopefully sometime this month or the next). Good luck with your Moltres Raids, Trainers!