»Edan«

Look at this! The two vampire wearwolf thingies that Persephone kills right before Neo is "introduced" to the key maker are called Cain & Abel. That is similar to your garden of eden thing, and that would also explain why the Architect was so P.O.ed about the flaws of humans. The human "sin" got them banished out of edan.

Why Garden Eden? Because of the names? So if Cain and Abel are the original brothers then who is the Merovingian (= their master) originally?

Cain and Abel being the top henchmen of the Merovingian is akin to them being Adam & Eve's first two sons from the bible, making Mero and Persephone the same as A&E thrown out of the garden of Eden or matrix v0.1alpha like some have insinuated. Persephone could still be the mother of the matrix this way, by being a figurative first woman in the matrix, or by searching for some forbidden fruit that turned out to be the answer to the system failures. Very interesting...

And Abel is the one who got shot.

The Wachowski Brothers are huge comic book fans.
In one of the best comic series ever, the Sandman, there were two characters in the dreamworld named Cain and Abel, and Abel got grusomely dispatched constantly.
Also, the main character's name is Morpheus, but after he "dies" he returns as Daniel.
Biblically, Daniel is the dream interpreter for King Nebechanezzar of Babylon. Also, in the game, Morpheus has a phone message box that answers with, "Welome to the Daniel Institute of Dream Interpretation..."