You are sidelining him if he doesn't interact with the mainstream versions of other heroes. At the end of the day, what makes good writing is interesting relationships.
There's nothing wrong with Miles being in 616 and only working alongside Peter some of the time, a la the Bat-Family, which has most of the heroes operate solo in the same city. Not every issue of Batman features Batwing or Batgirl, but they can team up for bigger storylines or call on each other in times of need. That's enough for a "family." In fact, Batman is still known as "loner."
This has literally already been mapped out by so many other comic book franchises.
Miles's dynamics with Peter, Gwen, etc. need to be fleshed out more, but that's easier to do when they have easy access to one another.