So Cut Too Deep has Classic and 5Ds as heavily implied different dimensions instead of 5Ds being the future. Other stories, however, have it more nebulous. I personally have struggled with what I want, because I still hate Domino City being torn apart yet I love the 5Ds characters and want the ones we see in the show to be the main verse ones, which would mean it has to be the same timeline. I have some readers balking at this while others are okay with it. I finally came up with a way that it could be the same timeline and be more satisfying to me. This idea is as follows:
With the Classic characters forewarned on Zero Reverse, they prepare themselves and Seto refuses to have anything to do with Ener-D. Of course, Iliaster finds another route for it to come through. Zero Reverse cannot be prevented, although the Classics try, but at least they are able to protect themselves and others and evacuate the city as much as they can, although of course not everyone is saved. Yusei's parents still die and Domino and Satellite still split. Seto tries to fight back against the rules Rex Goodwin wants to set up when he mysteriously arrives and assumes control of the fractured city, but even Seto's power and clout can't overcome Iliaster's hold. Atem, Yami Bakura, Seto, and the Big Five try to use their magic, but it doesn't seem to work against these enemies. The Crimson Dragon visits them and tells them he will bestow his powers on the Signers and they will be the ones to topple Iliaster in a few years. The Classics will have to be patient and wait until then, and not interfere with the Signers' current lives, as how they grow up is important to what they become. So the Classics resume their lives as best as they can and bide their time until the Signers can come into their own. Seto develops Duel Runners, knowing they are important to the future even though he's still not sold on the idea. 5Ds proceeds as in the show, with the Classics stepping back to allow the next generation of world protectors to have center stage here. Meanwhile, the Classics have other enemies to deal with.
I have introduced this idea in the stories, although only basically and I haven't yet shown all of these details in the stories. For me, this is the only way to make the series the same timeline and have it anything satisfactory at all.