Super R-Type had excruciatingly hard bosses. Dr. Robotnik in Sega 2 was, as you say, retarded. Not only did you have to beat a fairly annoying metal sonic first, but the boss fight after was long and painful. I'm certain I did beat it with my pal, though.
My personal suggestion would be Vega, Sagat or M. Bison on level 7 in the original Street Fighter 2. Fuck, spent so much time grinding it out to beat those motherfuckers
I'll admit that I was pretty young when I was playing Final Fantasy Legend 2 so I probably didn't know the difference between different stat weapons and such. Game was still super hard and nothing before Venus even came close to the amount of rape she dished out.
And if I remember correctly there was an issue with not being able to go back to get better supplies or whatever after saving near Venus.