Michaels won 14 WWE championships, Benoit won 12. Michaels won 4 WWE World Titles, Benoit won 1. Michaels won 2 Rumbles, Benoit won 1. Michaels won 14 Wrestling Observer Newsletter Awards, Benoit won 15. Michaels is a WWE Hall of Famer, Benoit should be. Both are in the Wrestling Observer Newsletter Hall Of Fame. Michaels won most of his championships in the WWE. Benoit won championships all over the world. Michaels has never been chosen "Best Technical Wrestler" by the Wrestling Observer Newsletter. Benoit was chosen "Best Technical Wrestler" 5 times by the Wrestling Observer Newsletter. Michaels won 22 championships during his 25-year career. Benoit won 35 in his 21-year career.
Looking at it strictly by material accomplishments, they are pretty even. All of Michaels' big accomplishments happened in the WWE only. Benoit was successful everywhere he wrestled, all over the world. Michaels would get the slight edge because he won more World Titles.
Benoit's style was stiffer and a little more reckless than Michaels'. There were times Benoit's high-risk offense didn't pay off and he lost matches he should have won.
But I don't judge wrestlers by the number of championships they've held. If we go by just that then Jerry Lawler would be the greatest wrestler in the history of the universe; nobody else even comes close to the number of championships Lawler has held (162 by my last count; that's one hundred and sixty two!).
I judge wrestlers by their talents, abilities, and what they can do in the ring.
Chris Benoit was the greatest in-ring pro wrestler I've ever seen. Michaels is certainly one of the best of all-time but Benoit is THE best of all-time.
EDIT: You're wanting opinions on who was the better wrestler, meaning he won more matches without cheating and shortcuts, and which is the harder one to beat without cheating and shortcuts.
Benoit was the better offensive wrestler, meaning because he was so talented, had so many skills, and so many different ways to wrestle, he didn't need to cheat or take shortcuts, he just flat out-wrestled his opponent, sometimes mauling and beating on them (forearm smashes, chops, headbutts) at the same time.
The harder one to beat is Michaels, I think. You had to damn near kill HBK to pin him. His "will to win" was so strong there was just no quit in him. You pretty much had to knock him out.