Mother is more popular in Japan, and there's much more potential for a moveset than an F-Zero since you have to make one from scratch like Captain Falcon At least people know that Ninen comes from the first Mother game but other than that they do get some things wrong. Also when Lucas was revealed in Brawl, nobody asked for him as a playable character. And was very underwhelming for most people since they did not know him other than being in the same series as Ness. I mean EarthBound gets more exposure nowdays than F-Zero, such as a cult fanbase, the Mother 3 memes, Reggie asked about Mother 3, the Avgn Video, Game Theory's Ness video, UnderTale and Chuggaconroy's currently running Replaying EarthBound LP. Some people think that F-Zero is sort of an outdated racer, while EarthBound is a timeless classic and became an essential Snes game by retro fans. There's more exposure for the Mother Series outside of the Super Smash Bros. Series.
We can't see the sales of EarthBound on VC. and the original release sales figures isn't very reflective of today's Mother Series other than somewhat neglected, but not Obscure. We know it sold well from what Nintendo said about EB on VC, or else they wouldn't release EBB.
Currently not ALL F-Zero stages are confirmed and people aren't expecting them to return, while the Mother Series has all of their stages returning from previous titles and the Rambling Mushroom was confirmed to be in the game, Ness and Lucas has some friends in their Final Smash. We could be getting about 5 additional trophies in Ultimate when including the Rambling Mushroom item and the Final Smash characters I'm not surprised that Sakurai seems to favor the Mother Series over F-Zero. Sakurai could've easily chosen not to include Lucas in Brawl because the game wasn't released in Japan. He didn't even want to emphasize Japanese-only characters. Maybe why he cut Lucas at first in Sm4sh, but did make him DLC later on because fans wanted him back.
It's also worth noting that when F-Zero and EB had the same amount of representation in Sm4sh, the Mother Series had at least 2 Smash Run enemies: The Starman (Also an assist trophy), and the Devil Car from Mother 1, F-zero had none. A similar case happens with the fact that Porky was a boss in Brawl along with the Porky Statue appearing in the stage. F-zero only got represented from the Blue Falcon and Captain Falcon himself in Subspace. In Melee and Brawl respectively, the Mr. Saturn item (Can be plucked as a very low chance for Peach's Turnips), and Franklin Badge (Also an item you can put on in the Special modes) were put into the Smash Series. F-Zero did have a stage you had to run through in Adventure mode.
In the Extravaganza Video, they also drew an image of this for Ness...
People are pretty much knows why it has more representation than F-Zero and made a post in reddit a while ago but some aren't okay that it has more representation.
https://www.reddit.com/r/nintendo/comments/8cdswj/so_why_does_the_mother_series_get_more_smash_bros/
https://www.reddit.com/r/smashbros/...y_does_the_mother_series_get_more_smash_bros/