Trump will complete his purchase of the Doral course in June and has hired top course designer Gil Hanse to improve the championship course.
After another day of low scoring at the elite event on Saturday, with the scoring average 70 on the 72-par course, the 22-year-old McIlroy said he hoped the work would see some harder challenges.
"It's a resort golf course. It was a tough test 15 years ago but now it's just got outdated," said McIlroy who shot a 65 after blitzing through the front nine with six birdies.
"They definitely need to do something with it and it's great to see that Trump is taking over the place and he is going to do a good job with it, I am sure."
Englishman Justin Rose, who is three shots off the lead, tied for second with Keegan Bradley, agreed with McIlroy.
"I think in its day it was long but long isn't really a test for us anymore," said Rose.
"The greens have been soft this week and any time you put a quality field on soft greens you are going to get close to the hole and make putts and birdies.
"Obviously the greens are somewhat flat. I think that is why there are a lot of putts made on this course. I think someone told me a stat today, I don't know how they measure the stat but its the easiest putting course that we play. So that's why the scores are low."
But tournament leader Bubba Watson had a different view.
"It's very challenging. Obviously when you are playing good golf, someone is going to shoot a low score," he said.
"Next year it could be really windy but somebody is still going to shoot under par, that's just how golf is."
Watson agreed the softness of the greens had assisted the low scoring and said the wind this week had also been helping the players.
"Fairways are not as firm as sometimes, the greens are not as firm as sometimes.
"Obviously you can make it tougher and tougher but you can't make the 18th hole any tougher unless you just add another tee on the 17th green I guess.
"There are some holes that are really difficult, some are easy. Right now the wind is playing into our hands on these par-fives, three of them are somewhat downwind, so everybody is scoring on those," he said.
Rose said he hopes that Hanse, who has been selected to design the course for the 2016 Olympic Games in Rio and is widely respected as a course architect, would bring some improvements to Doral.
"I love some of the work that he has done. I think it is important to get the re-design right on a course like this that has staged so many fantastic tournaments. But I think it would probably benefit from a tune-up".