When Astonishing first came out it was so out of sync with the other X titles of the time that I believe many people dismissed it as not a part of mainstream continuity but rather a stand alone series to give whedon a crack at the X-Men. However after reading the wiki about it, supposedly after the completion which was very late because of the delays and often bi-monthly scheduling periods, it was somehow supposed to fit into regular X-Men continuity as sometime before Messiah Complex began. So what is the verdict viners? Is Astonishing 616 canon? or is it another universe?

It is canon.

Everything but Whedon's stuff just hasn't happened, really.

Its canon. Its just supposedly the adventures of the home team of X-Men at the mansion. The only thing is it doesn't tie into M-Day.

I think it's canon...

Once again, you are spot on.