The 13-team league was launched on Monday to provide context to fixtures played between World Cups.
13 teams, including 12 full members and Netherlands, will play eight three-match ODI series, four home and four away, over the next two years to determine top seven slots alongside hosts India at the 2023 World Cup, an idea that Atherton explained why he found quite "complex".
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"There is always logic in everything that happens, but what tends to happen is that it's incredibly complex because what you're trying to do is fit two systems together," the renowned commentator said on Sky Sports Cricket.
"You've got the ICC global events World Cup, World T20, and what was the Champions Trophy and you're trying to marry that with the usual bilateral series in what's called the Future Tours Programme where every team plays against each other. Trying to mix those two together is incredibly difficult, and you end up with this," Atherton added.
The quest of the ICC, whose planning for the league began as early as 2017, was to provide greater context to each ODI fixture played between the two World Cups.
Each win will result in 10 points, whereas a no result or tie in five points. The teams finishing bottom five after 24 matches each will have to compete for the final two World Cup slots at the global qualifier along with Associate nations progressing through the Cricket World Cup League 2 and ICC Challenge Leagues.
The whole qualification process covers 32 countries and does provide at least a chance for every nation involved to make it to the pinnacle event in India.
Atherton, however, said: "try explaining this to the man on the street, try explaining the World Test Championship to the man on the street, which we find it hard enough to understand and we work in the damn game, and then try explaining that to the man on the street."
"What you've really got to try and get is something that's less complex and a bit more straightforward in order for people to understand."
The first series in the league will be hosted by last year's World Cup champions, England, against neighbours Ireland from July 30 in Southampton.
(Inputs from PTI)