Well, I was thinking about some things on the timelines.
FRLG are in the same timeline as RSE.
The RSE timeline is different from the ORAS timeline.
ORAS timeline is the same as XY, and the fact that we have Professor Sycamore's assistants in Alola shows that SM are in the ORAS/XY timeline.
When we got to RSE, the frustration was big that we couldn't trade Pokémon from GSC/RBY there. Like really big. Now we can transfer Pokémon from RBY to SM, which should mean (by this logic) that the timelines are as follows:
RBY > GSC > ORAS > XY > SM
FRLG > HGSS > RSE
I don't know where DPP and BW/BW2 would be in this timeline, but, following this logic, Red's team should be the same as his GSC team, thus being Pikachu, Charizard, Blastoise, Venusaur, Snorlax and Espeon. If he gets a mega, it will be MegaZard X for sure, since that's what he has in the Pokémon Origins anime, although I'm not sure they will Mega Evolve anything in this game if they can avoid. I bet his Pikachu know the Z-Move and that's that.
About Blue/Green, Pidgeot, Alakazam, Rhydon, Arcanine, Exeggutor, Gyarados is his basic (without starter) team in RB
In Yellow, his team is Sandslash, Alakazam, Exeggutor, Ninetales, Magneton and Cloyster. Magneton, Cloyster and Ninetales are subbed out by his Eeveelution.
As gym leader in GSC, his team is the same as in RB, so if I had to guess what Blue's team would be, I'f go for the RB one, since it hits nostalgia right there.
XY never really was fully defined in the original timeline, even with that timeline that was officially defined a few years ago. It was just sort of ambiguously stated that XY took place around or after BW2.
Following your logic, though, we would have two timelines of
RBY -3 Years-> GSC -?-> ORAS = XY -?-> SM
FRLG = RSE -3 Years-> HGSS = DPPt -?-> BW -2 Years-> BW2
This makes sense if it's assumed that Mega Evolution isn't something that's generally known, particularly in Japan, and Steven spearheads the Hoenn interest following a discovery in France. That, at least, is potentially plausible. The issue is the Fairy-type, because types are defined by characteristics. Even if the Fairy-type was unknown to the point that it wasn't given it's own classification in RBY-GSC, trainers like Lance and Claire should have had more issues and reasons to be wary of pokémon like Granbull and Wigglytuff because of their physical characteristics, and how their dragons interacted with them. By the same token, the Magnemite could have been later classified as a Steel-type when it was noticed that it was hurt more on average by a Ground-type attack, but less by a Normal-type attack than a comparable pokémon such a Voltorb or Pikachu.
Still, this tie-in to the original timeline is an interesting theory.
On the other hand, we can portray the cross-generational travel of pokémon as a matter of time or space. Between Gen I and Gen II, it's a matter of time displacement, and is thus a two-way road with certain stipulations. Because this technology exists in this timeline, and yet it's not possible to connect either of these generations to Gen III, it could be stated that Gen III exists in a different deminsion of space.
Following this, we know that pokémon physically travel through space to get to the next generation (Gen III->Gen IV, Gen IV->Gen V). Theoretically, the pokémon could make a return journey to their home region, but they likely can't because that home trainer is no longer there, indicating that they cannot travel backwards through time. For context, assuming that a diglett is sent to Diamond from Fire Red, because we know that three years have passed since the diglett left the Fire Red trainer. At most, this means that it would take a total of six years for the diglett to return to Kanto. Likely, this is less, because we know that this same diglett can be sent to Heart Gold, and the departure and the arrival could both be in Fuschia City.
Finally, we know that RSE and ORAS exist in separate dimensions according to in-game lore, and wasn't it proposed that the meteor from the Delta Episode be sent to an alternate dimension? This, at least, indicates that across dimensions, the Pokémon World has technology that can affect both time and space, and this is proved by the fact that pokémon from the two dimensions that RSE and ORAS exist in can co-exist through Bank.
So therefore, it's entirely possible that Pokémon Bank is a sort of pocket dimension that is designed not to exist in time - it's meant to connect to every game for the forseeable future, even including games that would theoretically exist in a separate time from XY, ORAS, or SM. The caveat seems to be that there is a mechanism that prevents a pokémon from being accessed from a time that comes prior to it being placed within this pocket. We're not losing access to Bank from XY and ORAS, after all, it's just that from those games, we just don't have access to any of the pokémon placed into Bank by RBGY or SM.