Marvel Super Heroes Secret Wars #1 is clearly the 1st full appearance of the Beyonder. He appears in energy form, he uses his power to transport many of the Marvel characters away from Earth, he speaks, he destroys a galaxy, he forms a new planet, he even blasts Galactus knocking him unconscious, kicking off one of the best Marvel storylines of the 1980's. It also has the distinction of being a #1 issue.
Secret Wars II was a horrible storyline that was just painful to read, where goofball Beyonder forms a body and walks the Earth to try to better understand humans. No comparison whatsoever.
Marvel Super Heroes Secret Wars #1 is clearly the comic to own, with a huge potential of blowing up in value if Disney ever makes a Secret Wars movie. And by the way, it is already blowing up in value over the last few months.