Most MGS bosses are explainable in part by having some knowledge of applied science(The Pain used pheromones to control bees), are people that have the whole "your-body-is-the-ultimate-weapon" thing going on(The Boss, etc), have technology (The Fear's invisibility and Fortune's luck) or are simply supernatural(The Sorrow, Volgin, Psycho Mantis).
The only boss who's "powers" I couldn't take seriously (no matter how hard I try) was The End's photosynthesis. That beats even Liquid's "I can survive any exploding vehicle, so long as I try to kill people with them" ability in terms of retardedness.