Mother Brain's role and physicalities are what gave her/him/it's name: it is the leader of the Space Pirates and looks like a giant brain. However, in Metroid Prime 3, a cross-section (a fancy way of saying '2D map') of a "future Aurora complex" is shown, which looks nearly identical to MB's hideout in Super Metroid. Here is a quote from Metroid Prime 3, as taken from Wikitroid:
"Twenty years ago (prior to the events of Metroid Prime 3: Corruption), a team of Federation scientists announced the birth of an organic super computer. Its name was Aurora. Since that historic date, thousands of Auroras have been built and installed. Originally designed for scientific purposes, the Auroras are now used in government, business, and military roles as well. They are given male, female, or gender-neutral personas, based on the needs and desires of the staff at the facility they are to serve in. A vast network links all existing Auroras, allowing them to access a tremendous database without peer."
"The Mother Brain was built by the Chozo, though the manga indicates that the Federation had some part in this as well, as she was built to link the Federation and Chozo information databases, similar to the function of the Auroras."
So, we know that Mother Brain was built by the Chozo in collaboration with the Federation to link their separate databases together. Perhaps Mother Brain was a prototype Aurora Unit that the Federation built with the Chozo, installed on Zebes for the Chozo, the Space Pirates invaded, found MB, thought it was a diety, worshiped it and transformed Zebes into their base.
Perhaps Samus' mission on Zebes in Metroid/Zero Mission wasn't to just eradicate the Space Pirates' base, but to destroy the Aurora Unit that was on the planet, in fear that the Space Pirates would use Mother Brain/Aurora Unit to access the information in the Federation's database? At the end of Metroid Fusion, it's indicative that the Federation had sinister plans for the Aurora Units, so this helps add to the idea that Samus' mission was not what she had been told it was.
If Mother Brain was simply an Aurora Unit, and the Space Pirates simply invaded Zebes, found Mother Brain hidden in Tourian, came to worship it - or that Ridley claimed to have been given orders by the Aurora Unit (they are capable of speak, both audible and telepathically; telepathic speech to Ridley would help aid in a belief that he was insane) - then wouldn't Mother Brain actually be a false idol, and not the "first-in-command" that we have believe it to be?
The Federation was the one who told Samus Mother Brain was the leader of the Space Pirates. This could have been a cover-up to get her to infiltrate Zebes to destroy the Aurora Unit to prevent any form of data corruption on their end by the Space Pirates.
Call it a conspiracy theory or not, but it's a goddamned good one.
THOUGHT: We all come across random bits in the games we play that have us scratching our heads from time to time. I take these thoughts and try to give them answers, as well as you closure.