Not sure how well this post will age as I'd be amazed if I was right on the money with some of these suggestions, but for the eventual Diamond/Pearl remakes what would you like to see done in it besides just a graphical update and features from the newer games?
For starters, the regional dex would likely be expanded as it's a trend lately to have a huge regional dex. if that were to happen would be no excuse to not have no new (or just a few) more fire types.
Since walking with Pokemon has made a return, would like to see that in the remakes... but being more interactive like in Heartgold/Soulsilver as you can only make the walking Pokemon acknowledge you when you speak to it in Sword/Shield.
Some cues from Platinum would be nice such as Looker, Charon, and having a variant of Platinum's take on the Spear Pillar/Distortion World event. Considering that Giratina nabbed Cyrus due to not being pleased with his attempt at destroying the old universe and replacing it with his own, Giratina probably wouldn't be happy about what Cyrus did in the original Diamond/Pearl either.
As for version legendaries, I can see them doing a HG/SS and having one be available before the other. As for the status of the other one, would probably be part of a post-game episode much like ORAS Delta Episode. Maybe Cyrus making good on his threat of one day returning or something, such as having the version legendary you didn't catch.
Would like to see Arceus actually be plot-important or at least have more of a role. Maybe if Cyrus does make his return the post-game, whatever trouble he stirs up would be bad enough that a royally pissed-off Arceus shows up to dish out some Judgement. After that confrontation, the location of Arceus' temple is found which would be either around Spear Pillar or the Solacean Ruins due to the connection to the Unown established at the Ruins of Alph/Sinjoh Ruins. There not only would you be able to catch Arceus, but you can also have Arceus make a new Dialga/Palkia/Giratina like in Sinjoh Ruins.
As it's been revealed that even legendaries can have regional variants, it's possible they could add some Sinnoh versions. Mewtwo actually could work, as this is the region with the connection to the creation to the universe and it would make sense that the creation legendaries (whichever one is responsible for making Mew) did more than one attempt at creating Mew, with this Sinnoh Mewtwo being the natural counterpart to the Kanto Mewtwo's lab origins. I can see it being sealed away for enjoying a good fight too much for its own good. As for its typing, maybe Psychic/Dragon or something to reflect its connection to the creation legendaries.
As for what ultimately happens with Cyrus, he'll actually be arrested by the international police once his Pokemon are confiscated from him (probably won't happen but would be funny if Cyrus' confiscated Pokemon were given to you to keep). Heck, before his defeat I can see him going to Team Galactic and outright admitting to them all that he has no use for them anymore now that he wields creation.
Would also like to see the champion title defense from Alola to make a return here, with Cynthia being a new rival of sorts due to seeing you as a worthy foe. Heck, maybe even Elite Four members can challenge you, using a different set of Pokemon than their Elite Four battles to keep you on your toes. As for who else could challenge you, besides Gym Leaders and Barry maybe Lucas/Dawn (likely after helping them out with something so that wouldn't come out entirely out of left field), Cheryl, Mira, Riley, Marley (who I can see having a Gothitelle), Buck, and the Team Galactic Commanders should they genuinely turn over a new leaf (with some more varied teams to reflect that change). Heck, maybe a male and female Galactic Grunt as challengers because why not.
A Sinnoh wild area. Don't know how they'd introduce that but maybe a result of something Cyrus did, dunno.
And of course, would want the Battle Frontier from Platinum to return.