I rewatched the original series and then X-Men 97 and one of the things that stuck out was that in the original series Cable had a son named Tyler in the future that he was always eager to get back to whenever he had to time travel to the past, yet in 97 Cable just seemed to be reduced to Baby Nathan returns from the future as an adult. Cable is in no rush to get back home to his son. Obviously with Apocalypse around in present day, it's handy to have Cable on hand but the writers do currently have seemed to forgotten that Cable actually had a life and family in the future.
Speaking of Apocalypse, I think they are probably going to do an age of Apocalypse arc for the 2nd season. Given that Rogue was sent back to 3000BC to when Apocalypse was not yet Apocalypse, I wonder if Apocalypse is going to bring back Gambit as some weird twisted gesture to Rogue for helping him in some way in the past. I read somewhere that Wolverine became a Horseman in the comics to get his adamantium back, so maybe with Gambit potentially being Death (as he was in the comics), maybe Wolverine becomes War.
As for when Sinster abducted Jean to clone her, it's possible he may have grabbed some of her DNA during Beyond Good and Evil in which to make the clone, but I don't think he abducted her until the time skip between the two series as he didn't have the time or opportunity in the original series. The Phalanx destroyed his lab, forcing him to work with Beast and Forge, then when the matter was resolved, he high tailed it out of there. If Jean went missing, the X-Men would've immediately started looking for her, and it's not like he just photocopied Jean, making a clone would've taken a little bit of time especially if he was starting from scratch. I think he had the clone body ready to go and just needed Jean in order to upload Jean's memories into the clone. That way the switch would be quicker and the X-Men wouldn't realise a switch had taken place. The real Jean escaping was a wrinkle in his plan and he figured where she would go hence why he activated the Goblyn Queen when he did.