Del Potro was just 20 years old when he downed the Swiss legend 3-6, 7-6 (7/3), 4-6, 7-6 (7/4), 6-2, ending Federer's five-year reign as US Open champion, but the Swiss believes that he was the dominant force in that 2009 showdown.
"The only time when he was really better, in my opinion, was the fifth set. Obviously that was good enough to beat me that day," said Federer on Monday after seeing off Kohlschreiber 6-4, 6-2, 7-5.
"I felt like that I left that match with a lot of regrets. Probably feels like one of those matches I would like to play over again.
"Feel like I would probably win it somehow because I should have been up maybe two sets to love."
Federer leads Del Potro 16-5 in their head-to-head record although his win in Miami this year represented the first time the pair had met in four years.
Despite his disappointment at losing the 2009 championship match, Federer admits that having also defeated Rafael Nadal in the semifinals, Del Potro was overall a worthy winner.
Federer had already won the French Open, to complete the career Grand Slam in 2009, before going onto to win a sixth Wimbledon.
He also became a father for the first time.
"Making the finals here was actually a good run. But it ended my five-year reign in New York," he said.
Federer believes that had Del Potro remained fit he could have become world number one after that breakthrough.
For Del Potro, beating Federer should have meant he had the world at his feet.
Sadly, it was his wrists which proved the problem as he went on to undergo four surgeries.
After his 2009 triumph, he was to miss a total of ten Grand Slam tournaments.
At one stage last year, his world ranking, once as high as four in the world, slumped to 1,045 and he even considered retiring.
Federer said he was happy to see the likeable Del Potro back on tour and the feeling is mutual.
"I admire him, too. Everybody loves him," said Del Potro.
"It's going to be an interesting match to play. It will be the fitst time after eight years again in the central court of this tournament.
"I know how to play if I want to win, but always is a pleasure to play the greatest guy in history."
Now the 28-year-old hopes to recover in time for Wednesday's clash having needed to save two match points to defeat Dominic Thiem 1-6, 2-6, 6-1, 7-6 (7/1), 6-4 in the fourth round on Monday.
He even admitted he had come close to quitting the match as a fever had left him with breathing difficulties.
"I feel tired, but we cannot do magic," he said.