To the main argument though, it's a tough call. Everyone points to the classic battle for leadership of the X-Men, which happened under the circumstances OP required. There are a couple mitigating factors there though.
Storm didn't have her powers at all, and the way she was able to defeat Cyclops was by sneaking up on him and taking off his visor. She knew he would not risk hurting someone with a stray optic blast. Of course since then, he's learned to fight with his eyes closed, so that wouldn't be an issue for him.
The other issue is the retcon they provided to explain how that could happen. Madelyne Pryor wanted Cyclops to retire from the X-Men, so she psychically manipulated him to give up on the fight. He didn't even know she had psychic powers at that point, and trusted her completely, so she made him throw the fight so she could get him off the team and all to herself. The fight can't be used as evidence for these reasons.
Now, while Cyclops has become a brilliant tactician, the Danger Room is where he's most at home (well, it was, let's not forget it's a sentient female robot these days) and currently [i]relaxes[/i] by fighting dinosaurs in the Savage Land for fun, Storm is no slouch either.
Long before her past was retconned to include Wakanda, she was sufficiently skilled in hand to hand combat to defeat Callisto as well as Marrow, both of whom have powers which would specifically enhance their standing in a hand to hand fight. She had a fairly lengthy period where she was depowered and held her own splendidly against various powers opponents. I'd honestly say they're about equal where hand to hand combat is concerned.
I'm going to assume neither of them is in control of the Danger Room. The only thing I see giving either of them an advantage is the day of prep time. Cyclops is a character to whom prep time is very, very valuable. Like Batman, The Punisher and Doctor Doom, if he's had time to prepare for the fight, he's going to win it. And he's sufficiently paranoid that he's already started preparing for the fight even if he thinks it's unlikely. He's probably already planned out a scenario specifically for defeating Storm in hand to hand combat. 24 hours to prepare would allow him to refresh and further specialize it.