I don't know. The timeline is fine. It's just the story that is messed up with its loopholes and what not.
There are a lot of mysteries set inbetween each series and with it came forth a lot of speculation and assumptions. This probably led to people thinking the timeline is messed up due to differing perspectives.
IN GENERAL: One way isn't the only way. And the only way isn't one way.
Don't forget that only up to X5 is canon for the X series (ends with the death of zero, and then his discovery in MMZ). After X5 was over Capcom bought out the rights to the series from the creator and kept making games. X6-8 are not part of the original story.