Ridley gets shoehorned in as the final boss, when he really didn't need to be.
So, on the Metroid series in general, I kind of blame Prime for the shift away from "Mother Brain was the leader of the pirates and Kraid/Ridley were her generals" to "Mother who now? Ridley was always the one in charge! What's a kraid?" Due to Retro cutting Kraid from the game and not following through on initial concepts of having Mother Brain around, Ridley was the big bad of the game, and cemented him in the minds of the modern toxic meteoroid fan. This was only accentuated by Metroid Fusion, which is, eh, whatever. Fusion in isolation was fine, but dual-released with Prime, it just compounded things. This is all despite the fact that if you read Prime's manual and in-game scans, they go out of their way to make note that Kraid is just as important as Ridley, and is the one staying on Zebes to lead the rebuilding effort.
Zero Mission just made this worse. Not in and of itself, though the post-game boss being metal-Ridley didn't help things, but mainly the tie-in manga, which, while propping up Mother Brain a lot, made Kraid a mindless beast and placed super importance on Ridley, making Samus' fights with him a personal vendetta, as he was the one who murdered her family. So Mother brain is now an intelligent ai that is Samus' surrogate mother who has been corrupted by the Space Pirates, and Ridley is the real one in charge, and is the one who has haunted Samus' dreams since childhood.
Corruption just furthered this even more with all the aurora units, making Mother Brain no longer a unique being and now just, like, one of many super-computers of that type, while having many cinematic fights with Ridley. Kraid was also eschewed for a robot-not-kraid, even though Bryyo is arguably the most lore we've had for Kraid in the series yet, even if it's all inferred.
Then Other M comes out, and, once again, makes it all about fucking Ridley, even giving him a cute adolescent mascot form. Jesus fuck. Mother Brain actually gets some character development in this one, but, once again, is just an AI gone wrong, rather than an actual person with intent.
Fed Force features a "Master Brain" with no explanation, furthering the concept that Mother Brain is just one of many of this type of thing.
...it's hard being a fan of Kraid