1. Emperor Ing: This boss (and I'm including his two phases) pretty much acted as the truest final exam to the Echoes experience possible. Each segment had you utilizing a different acquired functionality or tech from the arsenal. The fight even re-introduces the tension that was originally Dark Aether's goal via the second form (Chrysalis) through a mix of phazon enhanced dark aether climate/poison gas emitted from itself and changes the shape of the fight to another ingenious use of the morph ball. The final form gives us a fight full of athletics and a faster pace with the Mutated Emperor Ing's unstable heart polarity requiring a good sense of management to disable before harming it and its larger and more lithe form requiring more spacing and movement to overcome and suppress.
2. Quadraxis: To be honest, this was almost number one but I felt like the little thematic influences behind the Emperor Ing battle really pushed it over the top despite Quadraxis being a similar test of every ability you acquired up until that point. This fight is made even more tense considering that there is no Light Suit to defend you from Dark Aether's environment for the entirety of the fight. It is still one of my GOAT encounters in a game in all 20+ years of me playing games though, with the way that you just enter the arena to the scene of the figure in the near distance and have the elevator lower you to ground level so you get a sense of its scale relative to Samus' line of vision.
Then you get to be the kid who takes the Lego set apart piece by piece. It's fucking brilliant.
3. Meta Ridley (Corruption): BEST. RIDLEY. FIGHT. EVER. Stylish as all hell (you are falling down a generator shaft 30K meters above solid ground or whatever else [I should fall the whole distance down one time and see what's down there] fighting the returning Prime Ridley Gandalf v Balrog style all while avoiding Ridley's crafty ways of snacting you up and toying with you the whole ride down. He knows he can leave at any time thanks to him having wings and you know that you have to put him down immediately to prevent this. It leads to an interesting situation where Ridley is just trolling and you're just trying to put a stop to that. Also has what is my second favorite boss defeat animation in the series (behind the original GCN version of Samus getting the Phazon Suit out of the Omega Pirate's corpse in Prime 1). This fight was an early taste of what one of the GoAT controller options [r.i.p pointer controls] could do for games all while being a complete rush from start to finish.
The only thing I have to criticize it for was for making the later Ridley fight seem so boring. If only there could have been a switch between the two so this fight, now sequenced as the latter fight, would require more firepower/involved tactics/lasted longer. :lol
4. Dark Samus 2: In a similar vein to the above, Dark Samus 2 in Sanctuary Fortress was another one of those thrill ride fights where half the experience was in the scenario. Having
a battle with yourself (no wait, that's wrong;
this is more like it) up an elevator shaft in this crazy Blade Runner meets Tomorrowland environment as Dark Samus goes in for the kill with a far more matured combat repertoire?
There there's all the little nods to future (both by game date and position in the story line) Samus abilities rampant in Dark Samus' move set in this fight which include the Shinespark, Mockball, and Ice Missiles/Diffusion Missiles.
Did I also mention that the arena is a destructible environment that almost gives out completely during Dark Samus' assault?
Did I also forget to mention the immensely memorable introduction to this fight where you enter the base floor of a totally different area of Sanctuary Fortress somewhat isolated from the other zones and watch immediately as Ing possessed Dark Pirate Troopers fire at a figure that is seemingly offscreen before being completely #rekt by a piercing laser of Phazon which then cues Dark Samus into the screen, chuckling at their effort before going for chow time on the Phazon reserves?
Yep, this was a pretty awesome moment for that gen of gaming.
5. Rundas:
DAT. MUSIC.
Despite being setup for the fall, I always felt like the Hunters that assisted Samus in Prime 3 were all very unique designs with really interesting lore behind themselves and as such, it kinda sucks that you knew pretty early on that you'd wind up murdering every one of them. Rundas' fight in particular is this awesome audio-visual festival though. The theme speaks to his documented pride and the sad fate about to be bestowed upon him despite the brilliance of the fight at hand. The actual fight is all about being nimble and trying to peg a guy zipping around hurling anything from annoying Lucy aiming at Charlie Brown accuracy speed shot snowballs to Antarctic sized glaciers at you all at a moment's notice. This fight was also really cool for showing that some of the game's designers still came from that Echoes state of mind with how you had to manage stunning him, running towards him to pull off his icicle battle armor them shoot at his exposed body. It would have been neat if you had a segment where you had to rappel off him or haul him off an ice floe as he traveled around the stage, but that's just me and my desire to see the technicality/complexity of the fight increased.
Runner Up: Spider Ball Guardian/Harmony Class Drone
Yeah, I know some call foul on this one because he does stupid damage in the GCN version and the high damage glare effect was kind of rough leading to situations where you'd lose stupid amounts of health and even die without realizing it, but the overall idea of a boss battle like this is nothing short of inspired.
On the other hand, the Harmony Class Drone is an exciting fight done from an entirely different angle while still adhering to the "innards of a pinball machine turned death trap" design. The way the fight ramps up with each ascension upward is so cool and I will never get tired of boost ball launching off spider ball tracks.