I hadn't thought to compare Shooter's level of maturity as a writer to that of Hamilton or anyone else's. Still, it's an interesting comparison. Hamilton, as an older and much more experienced writer, did bring a certain level of expertise to his stories, particularly from the 330s onwards. If anything, his ideas are much more focused and "reigned in" than Shooter's. Shooter, like many young writers, wants to throw in everything, including the Kitchen Sink (your apt description of 350-51 notwithstanding), and 349, with its trips back to multiple time periods, is a good example. This approach gives his stories a diffuse quality that's hard to control, hence the repetition of the Legionnaires getting into danger just before Rond yanks them back to the present.
It's hard to imagine Hamilton writing such a complicated plot, though his stories certainly had their weaknesses.
As for other writers dividing teams into smaller units, just because they did so does not make Shooter's approach any less repetitious. It's been years since I read Gardner Fox's JLA stories, so I can't say why they may have worked better than Shooter's or even if they did. Perhaps it's because Fox, like Hamilton, had many more years of living and writing behind him. Perhaps they don't hold up any better than Shooter's did.
Agree that Shooter had enormous skills as a writer even at this young age. For one, he makes the reader care about the characters far more than Hamilton or Siegel ever did.