Metroid Prime 2: Echoes

[OB1]

All metroid games (2-D) have a singular time line (Zero to 4). The 3-D ones, so far, have taken place in other time lines, or like I said, I side story.

It's 1-4, unless you think that Metroid 1 takes place after Metroid ZM. The Metroid timeline is not set in stone, they only started to really care about the story starting with Metroid Fusion. Metroid 2 is the only game with the number in the official title, while Super and Fusion had them in the opening credits. I wouldn't be surprised if the sequel to Fusion dropped the number. And you say "3-D ones" when we don't know when Prime 2 is supposed to take place. Right now I believe the developers are trying to piece the whole puzzle together and have the story make sense, with the 3-D games helping with that rather than just telling side stories.

Also, if DJ is correct and Nintendo does want Metroid 1 considered as Metroid 0 from now on, and Metroid Prime as Metroid 1, then your whole side-story theory is completely wrong. Like I said, it looks like Nintendo is trying to fit the pieces together right now, and they could be changing the numbers or completely eliminating them in the process.

Intelligent Systems IS Nintendo. Retro is a company that Nintendo bought to use right now, they could drop retro studios next year. But Intelligent Systems is actually a part of Nintendo's in-house development.

Nintendo could just as easily dump IS as they could Retro. They are both first-party development studios, as much a part of Nintendo as EAD is. Retro is not a second-party like Rare or SK was, they are 100% a part of Nintendo. Iwata said so himself just a little while ago.