Ronaldo won the Pichichi award last year after finishing the top scorer in La Liga, but Messi enjoyed the more successful campaign as he helped Barcelona to success in La Liga before putting in a man-of-the-match performance in the Champions League final victory over Manchester United.
Guti, who ended a lifelong association with Madrid last summer when he signed for Bestikas, believes that marks Messi out as the superior player.
"[Ronaldo] is a great player and has been decisive in many games," he told Punto Pelota, "yet in the big games he doesn't deliver, which is something that Messi has done. The top stars are the ones who perform in the top-level games."
He added: "Real Madrid have yet to reach Barcelona's level. It will be very hard to beat them if you line up all players against each other one-by-one.
"We didn't care about bringing players through the youth ranks. We spent money on buying new players rather than creating our own. The biggest sadness is that I see Casillas is the only youth product in the team."
Guti also revealed he is unhappy about the way he left the club after almost 25 years' service.
"My treatment was a bit cold," he said. "I expected more. Over the past year, they could have contacted me to arrange a date for me to go to the Bernabeu and say goodbye to the fans. It hasn't happened and I'm still waiting for that call."