It's ironic that Star Fox has continued on with constant misfires while F-Zero has not. You figure the series that got the lousy game out of the deal would be the one to get mothballed. But maybe the problem is that F-Zero's standards have remained too high and Nintendo isn't interested enough in the series to put in the effort required to meet fan expectations. This was the chance to transition F-Zero into a mid-tier budget series but Sega buggered that up by raising the bar even higher!
To be fair, before Star Fox Zero I doubt that franchise's installments were big enough failures to consider mothballing it, unlike F-Zero GX sadly.
Only Star Fox Assault was really a premium product (Namco developed); Star Fox Command was a partial reimagining by Qgames/EAD of the then-unreleased Star Fox 2, the 3DS remake game was again a team-up with Qgames, and Guard probably would have gotten different branding if they didn't have Star Fox Zero in the pipeline.
Sure, Assault also underperformed, and was a co-production as was F-Zero GX, but I think it may have escaped scrutiny because it released so late in the GameCube's lifetime. And even then, we still know Nintendo at least attempted to get Criterion to do F-Zero, and have given the franchise nods in Nintendo Land and Mario Kart 8.
I guess what I'm saying is, F-Zero hit a few more speedbumps down the road, but the Star Fox franchise hasn't made massive amounts of progress since 2003 either. Only it did get luckier in developing a HD era game than F-Zero. Which is a bummer, because I like both series, and kinda hoped the Retro Studios F-Zero/Starfox cross-over was real.