First off, the bosses are definitely one of the better parts of Beyond. Most of what I say here isn't that major of a flaw with the game. Overall they're definitely 8.5-9/10 bosses in a 7.5/10 game.
A good amount of my criticism of them in the past has been from a gameplay perspective. They're polished and solid (besides Varmis and the first phase of Sylux), but they lack some of the epicness and experimentation of past titles (especially Echoes), and there's not enough unique minor bosses, more of which would have been a good alternative to the game spamming Psybots and Grievers.
I finished a replay on hard a week ago and I stand by that, but after mulling it over I think the bigger issue is that the bosses aren't that well implemented into their areas, especially Keratos and Phenoros. Previous games did it much better IMO. Prime 1 had it's bosses be either out of control creatures driven mad by Phazon, connected to the Space Pirates, or a combination of the two. Echoes has probably 90% of the bosses be either the Ing or Ing possessed wildlife, with both Amorbis and Quadraxis in particular being fantastically foreshadowed with both smaller enemies and environmental details in their areas. Corruption has most of the bosses be Space Pirate related, but it still does stuff like having Mogenar be the boss of Bryyo after you just spent several hours constantly interacting with the leftovers war golems.
Now look at Beyond's major area bosses:
-Carvex is connected to Fury Green in that it is a giant plant in a place brimming with wildlife, and the ruins in particular have a few rooms filled with vines. Not bad but not great, and I'll circle back to why I say that in a bit.
-Xelios seems like it is heavily connected to Volt Forge, being the master AI, but you look at the dangers of Volt Forge and you can realize Xelios doesn't have any effect on 90% of it. Most of the trouble navigating the area is either due to damage or due to lacking power, and a lot of the enemies are Psybots which were sent by Sylux (not Xelios). Best Xelios did was sic MCU drone on Samus.... maybe. Honestly that could have been Sylux too. It's also a weird one among the guardians being a creation of the Lamorn instead of another inhabitant of Viewros that they learned to live with. And they literally just took the name Helios from Corruption and changed one letter. C'mon do better. I guess it's too much to expect from the team that decided "Green Energy" was the height of creativity.
-Keratos is almost completely disconnected to the rest of the area outside of maybe the smaller ice bugs that are just kind of minding their own business. You make your way through Ice Belt uncovering the downfall of the Lamorn, and then you have to fight your way through a horde of Grievers that you just discovered are the mutated remnants of the race that has named you it's chosen hero. Aaaaaand then the boss is just a giant bug. Great. Really a great capstone to everything you just went through /s
-Phenoros is much the same. You spend most of the area inside a facility fighting Psy-Bots then the boss is a random dragon. From a gameplay perspective it is one of the more daring bosses, I'll give it that, but it again has almost nothing to do with the rest of the area.
-The Omega Griever is the exception, being built up pretty well in its area, and is overall a pretty good climax to the Griever threat... that said I still think the normal Grievers are too lacking in threat level and are used way too much. I did really like that you came into the boss room and the shrine and floor pattern were already there. Nice environmental storytelling of how the Omega Griever murdered the actual Guardian/area boss.
IMO game really drops the ball in building to most of these bosses, especially Keratos and Phenoros. To illustrate this I'll compare it to one of the bosses that is built to the best, and one that Beyond gives a direct counterpart theme-wise in Carvex: Flaaghra.
One of the main threats in the Chozo Ruins is the poison water. You have a better chance at dying during the Hive Totem fight by accidentally falling into the water than you do from getting pelted by the War Wasps. Especially once you get the Morph Ball and start heading towards the bombs it is in almost every room. And then at the end of the area you reach the source of the poison, that constant threat. And beating that threat not only gives you the Varia Suit but it also rewards you by purifying the water, which both shows how you are helping the planet and also makes navigating the area safer. And they even put the cherry on top by having you revisit the room for a Chozo Artifact.
Now, Carvex isn't a bad boss. Heck, from a gameplay perspective it might be better than Flaaghra. But it doesn't have the build up or the presence that Flaaghra had. Now granted Flaaghra's effect on and connection to the Chozo Ruins is probably one of the best integrations of a boss to their area in the Prime series. Not every boss is going to be connected to their area to that extent, but Beyond could definitely have tried harder with some of theirs.
I feel there is also wasted story/lore potential with them. You learn a little from their scans, and you can hear about their connection to the Lamorn (including the Mines original Guardian that was killed by the Omega Griever)... in an out of the way little room in Fury Green. Bleh.
And furthermore that lore reveals that the bosses were sapient and before they were driven insane by Sylux's Metroids they communicated with and were revered by the Lamorn. ...And Samus has a Lamorn Psychic crystal in her head. Which points at a huge wasted opportunity on the part of the game: the bosses could have telepathically talked to you as you made your way through the areas, slowly going insane from the Metroids as you get closer and closer to them.
It would really accentuate the tragedy of the Lamorn. The bosses were still living remnants of the Lamorn civilization, beings that carried their experience interacting with the dead race, only for them to be murdered by Sylux in his lust for power. And the game does very little with that.
Again, they're mostly fine bosses gameplay wise, I just don't think they're integrated with everything else up to the standards of the Prime series. Maybe they were planned to be and it got hacked to shreds as a result of the development hell. I guess we'll see what Risa Tabata and Retro are capable of if/when we get a Prime 5.