The thing about the notion of sequels is that to a certain degree, the nature of a sequel, and how good it would be, would depend on the game it's coming from. That is, GSC as a response to RBY is way different from BW2 as a response to BW1. A sequel to any region would be very different depending on the events of the previous games in that region.
GSC was very much about expanding the universe of Pokemon rather than expanding the story. The characters who have story arcs in it either have very general (and I would argue unsatisfying) arcs, or are fairly far removed from the player emotionally. For example, Red is little more than an easter egg. Blue went from nearly being champion to being gym leader, with little fuss about how that effected him. Only Professor Oak and Giovanni get anything approaching character arcs, and the latter only in the remakes as a few throw away lines.
No, the focus of GSC as an expansion was expanding mechanics and the way the world worked: GSC introduced items and breeding, and HGSS introduced the walking thing (which has been backtracked upon, natch).
The Unova arc is much different. Unova has been character- and story-driven from the start. We are in some ways secondary in the early game to watching Cheren struggle to exceed others' standards, Bianca struggle to meet others' standards at all, and N wrangle with opposing sets of standards. In some ways Unova is the first story in the series, as well, where these pre-programmed NPCs really attempt to engage with our feelings and opinions. Consider the constant questions about whether you have a dream, and whether you're satisfied with your choices.
Naturally BW2 followed from this, with complex and fairly satisfying character arcs for four of the major players from the previous generation: Bianca, Cheren, N, and Alder.
If we go back and get sequels for Johto, Hoenn, or Sinnoh, we can't expect them to feel like GSC/HGSS or BW2. Why? Because they're responding to different things.
To be completely honest, I only really want a Unova sequel. That is, I only want a sequel to the story of N. I would like to see a game about where N went after BW1. I would even try it if the mechanics differed substantially from the mainline games because I care that much about N. Another game set in or around Unova, that dealt with ideas from Unova, would be satisfactory. I want to keep talking about the ethics of Pokemon training. I want to keep looking at what you have to do to change yourself, or the world. I like the deep, psychological, even cerebral place that set of games went.
If I were to see sequels to DPPt, I would expect them to be very centered on power and the metagame, and I would expect them to deal extensively with themes of the pursuit of power, of societal use and distribution of power, and how people get their way. I want to see what happens to the remains of Team Galactic with a power vaccuum, without their culty leader.
If I were to see sequels to RSE, well, that's harder. RSE has a better plot than RBY/GSC in terms of development, but it wasn't very character driven. Wally's evolution was treated more like a subplot than anything. The theme of RSE seemed to be balance and the relationship between man and his environment, so I would expect a sequel plot to deal with that same idea. Still, the whole "we're going to pursue extremism until it endangers even everything we care about, then act shocked at our own stupidity" plotline has already been done and resolved. There's no room to really develop Hoenn any more along that line without drawing in elements from another region of the game.
Ergo, I would expect a RSE sequel to center on remnants of Team Plasma or Team Galactic operating in Hoenn, and I would expect Latios and Latias to be the central Pokemon. Those two groups made their bread and butter on extremism, and they're the only good fit for it. Magma or Aqua trying again would be trite, especially after both Team Rocket and Team Plasma have had a second go at it. Magma or Aqua or both assisting the PC in stopping either Plasma or Galactic would work.
Along that line, I think Plasma would work better for that story than Galactic, since the rank and file members of Plasma are portrayed as much more human, since the nature of the team after their first defeat has been set up, and the natural schism in the group welcomes discussion about extremism.
So, with all that laid out, here is what I would like to see in the next Pokemon sequel:
Villainous Team: Plasma splinter group still advocating the extreme separation of humans and Pokemon, possibly formed by, lead by, or backed by one of the Pokemon N was given as a child
Villainous Team Leader: One of the seven sages who is not Ghestis, Zinzolin, or Rood
Pokemon Professor: Birch or his child
Champion: May or Brendan
Prominent Trainers: Steven, Wally, Birch's Child, N, Hilda/Hilbert (as informed by memory link; Hilbert by default), Rosa/Nate (as informed by memory link, Rosa by default, or Nate by default if BW1 with female PC is linked but no BW2 is linked), possibly Cynthia, Barry, Dawn, Lucas, Red, Ethan, Lyra
How the main character gets drawn into the villain plot: Starter is stolen
Primary goal of the villainous team: Hack the graphical pokemon storage system and use it to release all captured Pokemon in the wrong regoin
Supplementary region: Sinnoh, where you must go to rescue your starter after defeating the team.
Plot: A splinter faction of Team Plasma advocating the forceful separation of humans and Pokemon begin abducting Pokemon in Hoenn, which has gotten less attention from powerful trainers in recent years. The Plasma faction is taking the Pokemon it's stealing, sending them to other regions, and setting them free, forcing the Pokemon to separate from their trainers. The PC would receive his or her pokemon before they started making major moves in the region, but quickly have their "starter" stolen. The whole game would be a quest to get it back before it makes its way to the port in Slateport, where it would be sent to another region. Or, possibly, you don't make it in time and have to go to that other region, likely Sinnoh, to get it back. Team Plasma's ultimate plan would be to obtain the source code for the graphical box system created by Lanette and hack into it, allowing them to steal all the Pokemon of all trainers in every region and set them all free in the wrong region.
At some point, they would actually manage to break into the system, and so your team would be locked to whatever you had out for the final portion of the fight against them. However, you would stop them before your Pokemon are sent to another region, or after only a small number of them are.
TLDR: A good sequel to a Pokemon game takes the really important aspect of the previous game and expands on it. Since Dppt was driven by Team Galactic, a good sequel would have to keep using Team Galactic. Since RSE was driven by the idea of extremism being bad, and since Team Magma/Aqua not learning their lesson would be stupid, an RSE sequel would have to have a villainous team from another region taking whatever they did before to preposterous extremes. Galactic wasn't really clear on its goals, so you'd have to use Team Plasma. Ergo, I hope to see a Hoenn-centered game where an extremist faction of Team Plasma has come and plans to hack into the graphical PC system created by Lanette to set Pokemon free in regions they're not from in order to prevent them from reuniting with their trainers, forcing separation between humans and Pokemon.
TLDR of TLDR: Extremist Team Plasma wanting to force all humans and Pokemon apart legit (and not just to create a power vaccuum) go to Hoenn and try to hack Lanette's stuff to mess up PCs EVERYWHERE.