Assuming they just update the models from the earlier Cyber Sleuth games I would like all the digimon lines from Hacker's memory to return as well as the inclusion of digimon from previous story games that were left out after they went from sprites to 3D models.
Having the Coronamon line to go with the Lunamon one, Dolphmon (aka Rukamon), Devidramon, Karatenmon, Kyukimon, Allomon, Kotemon and Anubismon are just a few that were in the dawn and dusk games that were missing from the Cyber sleuth ones which are not recolours off of the top of my head. That I think would go well if added back in.
Seeing some digimon that were not in dawn and dusk such as the Dobermon to Cerberumon line complete with it's werewolf (Jinrou) mode. Astamon (as an actual digimon not a medal), Witchmon, Buraimon (which makes a nice counter part to Karatenmon), Fangmon, Baromon and Bastemon would all fit in well somewhere with the ones already in the Cyber sleuth roster. None of these are recolours either.
Another thing I just thought of:
After the opening chapter of the game, Persona 1 gave players a choice between two different routes (the SEBEC route and the Snow Queen Quest) that had completely different stories and endings. I'd love it if a Digimon Story game did something similar. Like, for instance, they could have a Virus Busters route and a Nightmare Soldiers route and let players choose. This would make people more inclined to do a New Game Plus so they can see both storylines, and it could also give some more character development to groups like the Royal Knights and the Demon Lords.
This, as much as I enjoy the later Persona games I do miss this aspect to it and I agree it could work well in a digimon story game. However I would personally want something to do with the Olympos XII or maybe the four Great dragons versus the four Holy beasts if they could come up with a good reason for it.
I'd also like an ending that has meaningful consequences on the game's worlds and doesn't just try to retcon most of the story in a few minutes after you've just spent the whole time playing through it. Both Cyber Sleuth games' endings were disappointing, especially the first one.
Again this, as fun as I found both games the ending were a real let down for me. I really hope even if the digimon have to leave, which for once I hope they don't as I want to see an actual post game that shows the repercussions for that. I do not want to see everything reset via peoples memories being changed or worse the it was just a dream situation.
I just want the digital world to be the main hub instead of Tokyo. I loved Cyber Sleuth's locations and it made sense for the story, but I'd love to see a Digimon Story more deeply rooted in the digital world. I would also love them to expand on the farm from Cyber Sleuth
Personally while I can understand where you are coming from I would rather see a Mix of the two. Where story wise you have to go back and forth between the Digital world and Earth. A bit like Digimon 02 but not as episodic. I would also like both to be as open worlded as possible. And maybe visit other parts of Japan outside Tokyo.
Another thing I would like to see is a return of domination battles. The how and why would have to depend on the story but the general idea of it could still work I think.