It's really not hard to understand where disappointment stems from. A unique quality of video games is that their identity is forged in play, not just aesthetics or titles or names. Series earn their fans as defined by the way the game is designed and how it stands out amongst other titles. You can repackage more or less any game as any other franchise, but without that staple of identity in play it is, in reality, meaningless to the fans. Other factors play a part too, including aesthetics, but primarily when people say "I can't wait for the next Metroid/Half Life/Deus Ex/Final Fantasy/etc" they're speaking primarily of game systems.
So with Metroid you have a very clear vision of stage progression, exploration, and pacing. The initial out roar against Metroid Prime was satiated primarily because Metroid Prime, despite the perspective change, was structured exactly like a Metroid game. Metroid Prime has a lot in common with Super Metroid. On the other hand, a lot of the deep seeded, lingering hate against Other M comes not just from the emphasis on narrative, but how the game is designed from top to bottom. It diminishes upgrade based exploration and agency significantly enough for it to lose some of the "soul" associated with the series.
This is the vibe people get with Federation Fighters. There might be an incredible little game beating underneath the Metroid hood, but it calls into question why it's called Metroid at all when it doesn't appear to have anything in common with the series identity. Maybe it'll play differently than first impressions, but it seems primarily a co-op based action heavy game with none of the series strengths highlighted or discussed at all. This is in addition to adopting a chibi-like art style which is far removed from any other mainline or even spinoff Metroid game, further dissonance between the series identity and what this game is titled.
When stuff like this happens it causes fans to call into question why it exists under the current moniker seemingly (if not entirely accurately) at the expense of a mainline title that actually adheres to the series identity. Metroid: Federation Fighters is not Metroid 5 or Metroid Prime 4 in spirit. It's this bizarreo offshoot that might as well be reskinned and called F-Zero: Racing Rangers and you'd be hard pressed to have people say "why is this f-zero it feels like metroid". As a side, there is also this lingering concern with Nintendo that they fob off new entries in their franchises due to arguable poor investment (eg: now is not the time for new F-Zero or Metroid) but seem to obliviously release spin-offs wondering why people are upset and excusing the lack of mainline titles with "we're waiting until we come up with a good idea". It's a crock of shit and outright lie.
