Um, ok this is what happens. Metroid happens, Pirates defeated. Pirates go off in two groups, one to Zebes and one to Tallon IV. Metroid Prime takes place, Samus takes care of the Tallon IV group. Then Metroid II happens, Samus takes care of the Metroids, at this point there is only one remaining Metroid. Then Super Metroid takes place, Samus takes care of the 2nd Pirate group, the one on Zebes. At this point Zebes is destroyed. Then Fusion happens.......
Basically, Prime could not happen after Metroid II because there are metroid in Prime, and it could not happen after Super Metroid because in Prime both Ridley and Zebes still exist. By the end of Super Metroid both Ridley and Zebes are destroyed. What happens with Ridley is, he is killed in Metroid, resurrected by Pirate group 2 (Zebes group), then defeated but not killed by Samus in Prime (he is only blasted off of the temple), then finally killed in Super Metroid.