The main thing I keep finding myself trying to figure out is why Golden Freddy is more powerful than any of the others. Was he the first victim? Was he the oldest child? Was he actually not a child? Unlike the others who have to walk around in suits, he can fade in and out as he pleases, and his suit may not physically exist anymore, there's gotta be some reason behind it.
Theory: Golden Freddy is the most powerful (and this explains the final good ending minigame too), because he was the oldest kid, they were all murdered at his birthday party. The 5 kids couldn't move on until they finished their party. Golden Freddy's suit didn't have an endoskeleton, so he couldn't move, and instead just projected himself, while in reality he lay abandoned in one of the back rooms.
EDIT:
My ultimate theory of the FNaF timeline. Let me know if this leaves anything else unanswered, and I'll respond.
Unknown Time: Fredbear's Family Diner, contains Bonnie (aka Springtrap) and Fredbear (aka Golden Freddy). One child murder occurred outside the building at the hand of the Purple Guy, resulting in the Puppet becoming possessed.
Unknown Time: Freddy Fazbear's Pizza, originally contained the same 2, springlock mechanisms failed on Golden Freddy (that's why his endoskeleton was removed) and the suits were deemed unsafe and locked up, replaced with the main 4. At this location, during a birthday party (the birthday boy was the kid who became Golden Freddy) 5 children were killed by the Purple Guy, lured into the back room with him using the Springtrap suit. These children possessed the original 4 and Golden Freddy. Place was shut down due to health concerns and the murders.
1987: Freddy Fazbear's Pizza Generation II, staff attempted to repair the original four, ended up replacing them with the toys, Puppet and Balloon Boy were added. Purple Guy gets a job on the day shift, and repeatedly uses the Golden Freddy suit to tamper with the animatronics, eventually resulting with Jeremy being bit by either Mangle or Foxy on Day 7, during a birthday party. Employees guessed that Purple Guy was probably responsible for the tampering, but he was never captured. Location was then shut down.
1993?: Freddy Fazbear's Pizza Generation III, they move back to the Gen I location, original 4 are fixed up, location finally shuts down due to safety concerns as well as Phone Guy's death, which could have been caused by Purple Guy using the Springtrap suit, otherwise some other forms of foul play by the Purple Guy are likely too.
Interim: PG, using his Shadow Freddy costume, enters the old establishment and lures the 4 animatronics, one by one, to Springtrap's room, demolishing them. On the 5th night however, the Puppet helps the 5 children throw a birthday party, allowing them to finally be at peace, and the 5 kids confront the PG. In panic, the PG gets into the Springtrap suit, while laughing in triumph breaths on the springlock mechanism, disabling it and killing him. 6 kids (4 main, Golden Freddy and the Puppet) move on to the afterlife.
2023?: Fazbear's Fright opens, they use parts of the original 4 for the attraction, some of the toy animatronic parts are recovered, Springtrap is found. Springtrap, controlled by PG's spirit, tries to kill you, with you hallucinating the other animatronics, burned due to Phone Dude mentioning the fire risk. You survive and leave, the next day the place burns down and is destroyed. Springtrap is damaged but survives, as seen in the newspaper photo.
