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I have a (baseless) hunch as to why that may be. MercurySteam, the studio behind it, and subsequently Dread, first pitched Sakamoto on a remake of Metroid Fusion. Sakamoto turned the concept down, as he thought that Fusion needed no improvements at that age. Instead, he proposed that a remake of Metroid 2: Return of Samus would be more needed. Thus Metroid: Samus Returns was made. I am not too knowledgeable in game design so this may be fairly baseless, but I suspect that part of the initial pitch involved concepts and ideas for a Neo Ridley boss fight. If that were the case, it stands to reason that they may have attempted to utilize the work that they were proud of and Sakamoto liked in the game they ended up actually making. So they gave him a couple of cybernetics, sent him after the last Metroid, and called it a day. It would make the third phase of his boss theme, which has the tempo of Neo Ridley’s theme, a fun callback. Once again, I could be just way out there and overstepping.
what a weird way to end an otherwise great game. that ridley fight was there for no reason and makes super really weird, the metroid baby gets kidnapped by the guy samus killed like 20 minutes ago. samus returns is a really good game apart from that.