For reference, here is the timeline nintendo officially putout on the zero mission site. This is official, and Prime is right there. So Prime is canon.
http://metroid.jp/metroid_version2/history/index.html
Creators can change their minds? Prime 3 took things in such a different direction that I don't think it fits well with the games that would come after it if it was one canon. I don't get the aversion to that. Both universes would be their own canon and get their own games and be free to go in their own directions.
But the Prime games also have nothing to do with the main story of Metroid, so it doesn't make sense to include them in a timeline for this game anyway.