They were probably told the Nick comics couldn't contradict any important continuity of the show or do anything major with Shredder (he's left out of almost all the Nick comics but a few), so they couldn't go full Archie with them and do their own thing.
There's still some good stories in them, even if they're all essentially "filler" stories. As said the Rat King Vs. Monkey Brains issue is one of the best and was just like an episode of the show.
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