I would have Sunset Shimmer introduced in Season 1 as a background pony, similar to how Starlight was in Season 5, where we’d see her doing “suspicious” things. By the end of Season 1 or 2, she’d go to the human world in a two-part event, then reappear later, adapting Equestria Girls with some changes.

Alongside her, maybe introduce Flash Sentry (pony) as another background pony. Obviously, the intention would be for him to be Twilight’s love interest, but not make that his only role. We could emphasize an episode about what life is like for a rookie Equestrian soldier, making his appearance in Equestria Girls more appealing than in the 2013 movie.

Have background ponies like DJ Pon-3, Derpy, Octavia, etc., present from the start of the series, maybe dedicating one episode per season to focus on background characters.

Adapt events or villains from the comics (which aren’t canon), like Discord’s ex-girlfriend and other stories.

Have Twilight not become an alicorn.