As the Savage Land is apparently owned by Disney/Marvel, we could instead see Sinister running some sort of mysterious island and experimenting with mutations/evolution to advance mutants' powers even further. The various 'mutates' that Magneto had in the Savage Land could instead be Sinister's experiments. He could also have Havok and Emma Frost in captivity, having found Havok near the exploded mansion and rescued Emma from Trask's labs.

t:
that what i had in mind. Being in nature could be great for Storm and evolving her personna, it could be the first time she feel a real connection to it since she only knew cairo. And it would be all perverted by Sinister, we would have experiment on nature itself, the animals and mutant of course. There would be both technology, for Sinister, and something primal, tribal, with nature.
Going from Apocalypse it follow the theme of technology and it's limitation ect, wich is interesting to oppose to natural evolution or mutant evolution since they are connected to it in sole way, or so they think,we don't know, could be an hint for space.
I would more see Genosha and Magneto coming back in a third movie, he already has been there enough and they need to bring him in a subtle way. With the relation Quicksilver, i would see him leaving the X-Men at some point and going back to look for his father, he could then have the sale evolution as him in Apocalypse.
I really see it like this: first movie-sinister, island, nature, technology already. But start in the danger room and the mansion, to show a real school of mutant, all using their powers.
Second movie proteus and space, it evolve nice from the natural set up to go in a crazy advanced technology civilization, it can lead to some great question about many things. I really want to see it done with a dreamy feel, not too much time in space. It would be the weird episode, crazy but also psychologically and phylsophically chalenging. For Nightcrawler and his faith, comsic Phoenix force.The depth of the mind are the one of space, the inner and outer are the same and it could disturb them, feeling they were still not ready. A fleeting moment of love for Charles from another world maybe...
The final movie they go back from crazyness into space and find Genosha and lanny real political problems on earth. Magneto comes back, ... And it would end with an island made in space by Magneto for mutants, asteroid m. Wich would be a conclusion on theles of technology and nature and space, abit beetwen both worlds. I like what it represents and it would be coherent.
Of course along that you have Jean and Scott realtion evolving, the Phoenix rise why not. Also i would see another member to the team, like a younger maybe Kitty, she would be the fresh view since Scott, Jean, Nightcrawler, Storm and Quicksilver would already be well formed X-Men, at least the oldest. Also no more Mystique, she has disapear, maybe when she found Kurt was her son, and it would parallels the relation father/son Quicksilver is looking for. Having Jean and Scott becoming a couple and parents figure, they are lots of theme to dwell on. Also the relation of Charles and Ilandra would parallels there one, being so clear and love from the first sight sort of thing, when Jeand and Scott is more complicated.
I like Storm in the figure of mother nature and leader of the team, i would see her being in charge at the end of the trilogy. You star with nature and you end with nature. Cycle of life, and all the technology questions interesting, the danger room could be a thing, they are many things to go from with the X-Men
[As for nature and family i advice the movie The Witch, a pagan horror movie, really well made and thought]