I actually think we're in the fourth version of the matrix. The first was the Paradise version, the second was the Hell version. The Third was the one based on the cycle of the One (of which there were six instances). Since the function of the One (to maintain balance in the Matrix and Zion) is no longer an issue and those that want free can be freed, the rules of the third version no longer apply.
So, from my perspective
Version 1: Paradise-Failed
Version 2: Hell-Failed
Version 3.1-.6: The One-Obsolete due to the cycle being broken
Version 4: The Truce
Ok, so I've read that we may be in the 4th version of the Matrix at the moment, that the current version of the Matrix does not require the One (which we don't have one of anyway) to reboot the Matrix, and that the oracle wasn't brought into the picture until the third version (in which the One first appears). Given that, I have 3 simple questions: 1) Who is currently capable of rebooting the Matrix? 2) If when the Oracle was created the One was created as a remainder, then what is different now that there is no remainder (the Matrix was rebooted at the end of Revolutions, no?)? Smith shouldn't necessarily account for the One's opposite in the equation initially because he was simply an Agent before Neo pwned him in the hallway, then he changed. 3) Has anybody seen the Twins? Anybody at all? Sorry for such a long post