I would say Super has the best boss selection. Each boss and miniboss manages to be very unique from the rest. Fusion is a close 2nd, but it's bosses tend to be fairly simple and less interesting IMO. --- More villains need to be protagonists. BiS proves it can work. Ridley, Ganondorf, Fawful, Bowser, and Dimentio all for their own games!
Its between Super and Fusion for me. Metroid 2 only really had one boss. The Ridley and Mother Brain fights in Super Metroid are very satisfying and its cool how they offer a secondary way of defeating Draygoon. The fights in Fusion are all pretty fun too though.
Super had the best selection of bosses. Although Super Metroid bosses were easy, the fights were amazing in my opinion. The first Ridley encounter, Torizo, Spore Spawn, Kraid, Crocomire, Phantoon, Botwoon, Draygon, The Golden Torizo, The Second Ridley Fight, and The Mother Brain fights were simply epic. Fusion comes in second place.