It would most likely just make Goten into Future Trunks 2.0. He'd go through the same training as Trunks and in the case that one of the two died, the other would take on Future Trunks' normal role in the Cell Arc.
Let's assume for the sake of the scenario that both survive throughout those years. I'd still say Trunks would be the one to visit the first time, with Goten joining him the 2nd time around. This doesn't change too much at first, beyond #17 possibly needing to expend some effort to take down an additional Super Saiyan when considering the teamwork Goten and Trunks would have. Goku would still go in the Rosat with Gohan, with Goten going in with Trunks during his 2nd trip and Goku doing a bit of personal training with him in the days of peace. Overall, nothing major changes with the Cell Arc.
The present Goten being born far earlier would mean Trunks wouldn't have a natural lead on him and the two would be fairly equal in power and skill. This may allow Goten to win the kids' division. Regardless of the outcome, it'd make him far less of a lackey, so the Mighty Mask shenanigans don't happen. it would also mean they take less time in learning fusion, though not by enough to change the plot in a major way.
With the Zamasu Arc, however, things can take a somewhat different route. With someone just as strong as Trunks, it's most likely Dabura and Babidi would never get in the position where Shin's life would be in danger, so Zamasu is forced to look for a different timeline and is eventually dealt with by Daishinkan or Zen-Oh. As for the Tournament of Power, Goku and Vegeta not achieving Perfected Super Saiyan Blue would mean they are eliminated by Toppo or Jiren, with Universe 11 winning the tournament.
Assuming somehow Goten and Trunks still failed to save Shin, Goten isn't killed by Black prior to the escape and both Saiyans escape to the present timeline, we still have a new take on the arc. Whilst the timeline is being fixed, Goku would help teach the two fusion, as would their present counterparts. Once learning the basics, the fathers and future sons would go into the Rosat to perfect fusion. When returning to the future, Goten and Trunks would declare they will defend their future. In his base state alone, Future Gotenks is capable of manhandling SSJ Black, which forces the story to go one of two ways:
1. With their serious attitude, Gotenks quickly kills Black and Zamasu arrives to find himself outnumbered. His immortality still proves difficult, to which Goku decides to head back to the present with Goten whilst Vegeta and Trunks keep Zamasu at bay. Goku learns the Mafuba and with Goten there to assist him, he brings the right seal and seals away Zamasu. Still, without the power ups gained in this arc, Goku and Vegeta lack the strength to take on Toppo or last at all against Jiren, with Universe 11 still winning the ToP.
2. Gotenks leaves an opening for Zamasu to heal Black. Even with his Zenkai, however, Black is helpless against the fusion, his Rose form at best making Gotenks go SSJ. Zamasu and Black quickly resort to the Potara, with Gotenks using his full SS2 power to crush him. However, he is unable to last long enough to destroy Zamasu, at which point Vegetto steps in. Vegetto Blue makes the same mistake as in canon and diffuses too quickly, with the arc going the same as in canon from here.
