Detective Gumshoe started off as a scatterbrained but reliable ally to Phoenix Wright (defense attorney), even though he was usually under the thumb of Miles Edgeworth (prosecutor). As time went on, Gumshoe progressively grew ditzier and can't even solve simple logical problems, relying on Phoenix and the prosecutor of the week to solve everything.
Maya Fey grew incredibly ditzy over the series as well. In the beginning, she did all she could to help Phoenix on his cases, even if she wasn't always right, and didn't have any useful skills apart from the ability to channel her dead sister's spirit (which, due to her incomplete training, wasn't always reliable). Afterwards, Maya uses off the walls logic to justify her reasoning (which usually didn't solve anything and annoyed Phoenix) and always goes on about food at inappropriate times, turning her into a Cloud Cuckoo Lander.
Pete Wheeler of Backyard Sports. I mean, he forgot how to ride a bike within a few months of being a pro.
Batman: Arkham Series: Admittedly, Batman himself has suffered this trope due to a heavy case of Aesop Amnesia. In Origins, the dark knight learns that his I Work Alone attitude is not the way to go about his quest to end evil in Gotham City and eventually learns to form alliances with others in his life's mission. However, by City he absolutely refuses help from others such as Robin and Oracle, thinking that he can handle something small like an entire city-wide district of his entire rogues gallery all by himself in a single night. Then by Knight, Batman actually thinks that he can take care of the entire city being annexed by Scarecrow and the unpredictable Arkham Knight's forces on his own as well, while the rest of the Bat family stays on the sidelines and handle less important missions to help him. This gets taken to a high point hallway through the game when Bruce reveals that he's become infected by a disease turning him into the Joker and only has a few hours before his mind is consumed by it. When Robin offers to help him by handling crime for him while Batman remains locked up in a cell, he thrashes Robin and locks his sidekick up in the cell instead. Bruce informs his young ward that by keeping him trapped in a cell with supervillains running wild, this is the better option. Naturally, Robin gets captured by Scarecrow and used as leverage against the dark knight. Meaning that his loss to the Scarecrow resulted in his own poor thinking.
Yasuhiro Hagakure of Dangan Ronpa was never very bright, but over time his actions and dialogue become increasingly more erratic and idiotic. This is lampshaded in the following exchange between him and Aoi Asahina.
Hina: "What the heck's happened to you...? You weren't like this from the beginning, you know."
Hiro: "Well back then my personality hadn't quite solidified yet...!"
Yuna too although to a much lesser degree as it mostly takes the form of her naivety growing up on a small isolated island sheltered from life by her peers. It is also implied in-game that her new-found idiocy is due to the fact she is trying to imitate Rikku.
Perhaps it was just Kazushige Nojima's shaky writing (he admitted in an interview that he didn't do a lot of work on the first game and wasn't familiar with the plot/characters/cosmology of KH), but Sora went from often naive in Kingdom Hearts to often ridiculously clueless in Kingdom Hearts II.
This can probably be explained in-story by the fact that he just spent a year in a coma, having his memories and certain parts of his personality recompiled basically from scratch. You're bound to have a bit of brain damage from that.
Councilor Udina in Mass Effect 3 went from being a harsh, but intelligent advisor who supported Shepard's battle strategies for the very first time into a traitor who actually though that Cerberus was the organization that would save the galaxy. Keep in mind, Cerberus is also well-known for their catastrophic failed evil plans.
It gets worse in the spinoff game Persona Q - protein is mentioned almost every other time he speaks (in the P4 route, he even establishes it as the main thing he likes!), and a scene in the P3 side presents us with the notion that he's unaware as to what constitutes as sexual harassment. It's all the more bizarre, as unlike Arena, Q is set during September of Persona 3.
Tomb Raider has Larson Carraway, a hired henchman who has a redneck accent and wasn't too bright, but he wasn't a complete idiot either. By Tomb Raider Chronicles, his character is retconned to become even dumber (he tries to shoot Lara from a rooftop instead of letting her get the MacGuffin(s) so that their work is made easier) and his accent sounds like a redneck even more.
The Avatar from the Ultima series suffers an extreme case of this in Ultima IX, where he seems to have forgotten everything about Britannia, since he keeps asking about things he should know about since previous games. The most famous of these questions seems to be "What's a paladin?"
Sonic the Hedgehog: Knuckles. Ok, he was never the sharpest tool in the shed but that was more due to naivete and lacking sort of social skills, and even then had enough sense to stay on task and get the job done. Over time though, his lack of intelligence was played up to the sacrifice of all of his other traits which led to this trope. Almost all of his appearances nowadays(With the exception of his comic appearances) emphasize his lack of intelligence above all else.