Super Metroid is my favorite. Can do some decent sequence breaking, we get plenty of mobility from the start, and the game just doesnt seem to lose its fun factor after all the times i played it. AND we can get 100% completion without a trip to gamefaq; the X-ray visor reveal secret places.
Zero mission is fun too, some moments in the game can only be described as "spectacular", and bosses tend to be bruttaly fun. But.. 100% completion isnt possible IMHO without external help. Some hidden spots are way too obscure.
However, i strongly dislike Metroid Fusion; its brutal about its linearity. Everything does massive damage. All mobility moves like wall jumps and bomb jumps have been made useless. Cant get out of sequence and cant explore. Basically; it plays like a glorified Mario bros game with guns. Personally, i dont even consider it a "proper" metroid game.
The prime series are fun too, but controlling Samus in a FPS feels slow and doesnt have much in the way of mobility she shows in 2D. If only she could run faster.