Okay sorry this took a while to answer, I needed to put together my thoughts on this
Basically where I started with the 'Michael is Glitchtrap' theory is basically like. Process of elimination kinda?
I noticed that Glitchtrap didn't fit either William OR the Mimic. Glitchtrap is, well, not robotic from my perspective. He's sentimental for one (putting together the staffbots to look like the Aftons, the SL living room, Vanessa and Gregory directly referencing and paralleling Elizabeth and CC, etc), and doesn't really act like an ai program built to mimic things, unlike the Mimic seen in Ruin.
On top of that, Glitchtrap holds back. He has explicit rules; you have to find him, put his tapes together, and consent to merging with him (this is important). If this was William, he wouldn't bother putting together all these rules. Not only that, but Vanessa, Gregory, and Cassie are all still alive. And Glitchtraps appearance too- he's a costume, not a springlock suit. William always explicitly associated himself with spring Bonnie. Not the character, but the actual springlock suit itself.
Also, Glitchtrap knows things neither William nor the mimic WOULD know. The biggest clue is the Exotic Butters- how would William, and thus the Mimic, know about something only Michael would know?? And it goes deeper.
The color theory doesn't match up, either. William went from yellow (Midnight Motorist) -> purple (fnaf 2 and 3 minigames) -> yellow (springtrap). It's pretty clear that after William dies, he's associated with YELLOW now. His story is also over too, this was established with UCN.
Michael is sort of the opposite. The first time we see him, if you don't count fnaf 4, he's wearing purple. The next time in ffps, he's wearing yellow and blue. The natural next step is that he'd be associated with purple again. There's a LOT going on with the color theory too (yellow can mean both royalty and sickness, purple can Also be royalty and corruption, etc), in a way that connects to their stories.
Glitchtrap is purple; or, at least, his true form seen in PQ is. He's depicted as a costume deliberately; the yellow throws you off, it's not the truth. But take it off and you get a big black and purple blob. Not only that, it's a COSTUME. Michael has always, always been associated with masks, which are a part of costumes. William is associated with springlock animatronics, not costumes, even if they double as one, which says a lot to his own character.
Not only THAT, but everything since Help Wanted 1 and even the AR game has been referencing Sister Location, fnaf 4, and FFPS. Michael is the certain protagonist of ALL of these games, both directly confirmed or hinted at (yes fnaf 4 is Michael's nightmares after he actually got tortured by William post CC death, you'll have to tear this out of my cold dead hands). Michael is also repeatedly referenced in Security Breach, with the constant references to butters in sticky notes, again, only something he would know.
Also, of the main cast, Foxy is the only one that's missing. Foxy is VERY important to Michael and his character, and the different iterations of Foxy, especially Funtime Foxy and Ringmaster Foxy, are especially important. Yes I do think that each of the Funtimes represent the Aftons, and FT Foxy represents Michael. So we can gleam that Michael, similarly to his father, is a performer. He's the leader; the captain, the ringmaster, the older brother. This is hammered in with his monologue and the Security Logbook. This fits in exactly with Glitchtrap. He's theatrical, he performs, he pretends.
As for HOW Michael would've become Glitchtrap, I believe the circuit boards FazEnt got were from the computer in the ffps office. William is trapped in UCN, the Mimic was still trapped behind the wall in Ruin, and I don't think the mimic1 program existed at the time (not to mention Glitchtraps behavior doesn't fit mimic1).
Michael easily could've possessed those circuit boards on accident. You might be asking- well, Michael was dead, all of his Remnant would've burned up. And, honestly, I don't think he actually DID die at the end of SL.
Baby explicitly says "You won't die". The Scooper also injects Remnant into you, which is known to keep you alive and heal you. As for the rotting, that can easily be explained away as Michael literally being one giant walking infected wound. The scooper tore him apart stomach to throat, and Ennard went inside, tearing him apart internally. When wounds are bad enough, they rot, especially when they're left to fester and get infected. Besides, it would've been impossible to possess his own corpse. Remnant is best conducted by metal, not rotting flesh. And I doubt Ennard would've left enough of itself behind for Michael to actually control his own body.
So, Michael was likely actually alive and fully healed by FFPS. Thus, when he burned to death, he would've ended up possessing the nearest electronic things- the circuit boards in the computer. Whether or not he actually wanted to die (I don't think he did) matters; he possessed it anyways.
As for why he's now the main antagonist of the new games- well, I don't think he's evil. I think he's being affected by Agony.
Since the blob is one massive ball of leftover Agony from the rest of the animatronics, I think it's possible Glitchtrap has his own Agony too, especially if it's true that Remnant turns into Agony when burned up like I think it does. It'd explain why he's all black and goopy, since I believe Agony is described as a black, tar-like substance.
Some of Glitchtraps appearance would also be explained by Michael being him, such as the tears that are on the suit and his true form. Usually, lost souls are what have those tear tracks, like the dead kids. William has never been depicted with those same marks, EVER.
A lot of the above also explains why I don't think Glitchtrap is evil. I don't think Michael is fully sane, and Glitchtrap has a duality theme going on (purple and green are opposites on the digital spectrum). Plus, as I said, he actively holds back. He's cruel yes, and he's killed a fuck ton of people, but he sets rules and let's Vanessa, Gregory, Cassie, and for a time, Cassies dad, all live.
Also, he's a WAY more successful killer than William. He's smart, and while I wouldn't call William an idiot, he's not exactly good at hiding things. He's arrogant, believes he'll never die ("I always come back!"), he's theatrical to his own detriment, etc. Even in SL it was extremely obvious he was already being questioned, and was nearly caught and jailed. He died to CHILD GHOSTS. And Vanessa and Glitchtrap have never been suspected, not ONCE.
People really like to act like Michael is stupid, but he's FAR from it. He knew what was happening in SL, and pieced things together Really Fucking Quickly (in less than a WEEK). He also likely suspected Williams crimes beforehand, and if he hadn't in fnaf 1, he definitely figured it out in SL. He also very likely created fnaf 3; the building matches ffps's confusing labyrinth layout, clearly set up to burn down, the collection of Fazbear stuff, the audio lures, and the "to you, from working architect" in the security logbook. And then he helped Henry with the FFPS location, and possibly built the Rockstar animatronics (I say this bc it's a mix of Williams and Henry's styles of animatronics; the hard outer casing, extra abilities i.e. Freddy's coin thing, but they're cute, like Henry's, BUT the Michael thing is that they're.. well, Rockstars. I also think Michael made the plans for the Glamrocks but FazEnt stole them for these reasons lmao). Michael is far, FAR from an idiot, and all of these show he's actually REALLY fucking smart, likely smart enough that William felt threatened by him (part of why he was likely sent to the SL bunker). Glitchtrap is also clearly Very Intelligent.
Another part is that Glitchtrap doesn't hurt children. In one of the SB endings, on the newspaper it says 'missing locals', not missing children. Gregory and Cassie were never directly harmed by him either. Cassie was completely safe in the mall pre-Ruin, and Gregory seemed fine too, if possessed by Glitchtrap. It's never stated that CHILDREN are hurt, only the staff.
Also Glitchtrap is,, very sentimental. Neither William nor the Mimic would be sentimental about the Aftons, but Michael WOULD. He cares deeply about his family if SL is any indication, and would explain his favoritism towards Gregory, the CC lookalike.
Glitchtrap being Michael would ALSO explain why Cassies dad (aka bonniebro) was spared, long enough for the spirits in the staffbots to get JEALOUS. After all, what exactly makes him so special? He's Michael's old friend. Neither William nor the Mimic would care.
Also springtrap is consistently depicted as terrifying and beastly. Especially in hw2, where the place burns down and Springtrap hunts you down. William would've shown himself as the pinnacle of his inventions, not a nightmarish monster.
Oh, and another note, but almost every time William is in the game, whether in the background or not, Golden Freddy aka Cassidy is always there. Fnaf 1, 2, and 3 ('shadow freddy') follow this formula, but she's not there in fnaf 4, or SL, though I imagine she's not there in FFPS because William is already trapped, and for good this time.
The same goes for Michael and the Puppet/Charlie. Charlie is in fnaf 1 (implied in fnaf 2), fnaf 2 (the party Jeremy got bit at was for Michael), fnaf 3, fnaf 4, and FFPS. The exception is SL, but I believe it's because William is dead by then.
Notice how Cassidy doesn't show up past fnaf 3, but Charlie keeps showing up as the plushies. There's near constant references to her in every. Single. Steel Wool game. It's hard to NOT see it it's so often. So it's very likely Michael is still around, and only hammers in that he's likely Glitchtrap.
Also, writing-wise, it makes sense for him to become the new antagonist since FNAF was soft-rebooted. Typically the old protagonist is still important in soft reboots, whether that's as an important historical figure or the next games/series/movies antagonist, or a driving point for the next protagonist (think Peter Parker and Tony Stark). It also fits thematically, since it'd be a really weird spin around for the new villain to be an AI (doesn't fit fnafs formula) and having William be the villain Again would just be lazy writing.
Collapses. Okay I probably missed some things BUT. That's my main points. There's WAY more that goes into a much bigger theory (like PQ is Obviously Vanessa being freed from Glitchtrap, fnafs timeline, the ghost kids are back and are wanting to free Michael, the SW games are based on I Have No Mouth And I Must Scream, etc), but that's mostly what I have for Glitchtrap Michael.
Feel free to look up everything I'm talking about, I haven't bothered to put anything up but I have all of my facts straight. I've considered pretty much every other option in order to TRY to disprove my own theory, but every single new game and book only keeps proving me right unfortunately LMAO.
I've had this theory since like... before Ruin. I've had So much time to get everything straight. I'm sad no one else sees what I see lol.