Metroid Federation Force was just poorly timed I think. Much like putting in Bad-Boxart Mega Man in Street Fighter X Tekken, had the series not been at a low point/lull at the time, no one would really bat an eye. It's not like either game was a complete trainwreck like Sonic 06/Superman 64, although they DID have seperate issues, it wasn't absolute garbage. Seeing it as a mostly quirky thing or some harmless spin-off. With the lack of any "substantial"/main content, obviously more people are gonna feel burned.
Picking an unfitting artstyle also didn't help. Metroid, unlike Zelda almost always had a more serious or grounded artstyle. Rather than jumping between that and more cartoony styles every few games. Seeing how Hunters on the OG DS looked good for what it was, I think they should have made a sequel to that game instead, or at the very least, offered similar aesthetics. And mind you, Wind Waker failing to impress, regardless of what you think of the game(I personally like it, and Twilight Princess the most for the 3D titles), was a hit the Gamecube never recovered from.
Not that people should get as salty as they got, sometimes you gotta be patient. But I'm not exactly gonna comfort a corporation either.