No, he definitely has some blame to it. He still wrote the dialogue, and has admitted before that not only is he not a fan Sonic's female cast, he even tried to write out Sonic and Amy's dynamic in Frontiers. The only thing that's safe to say he's 100 percent faultless for was Rogue being covered up.

As already stated below, the Rouge outfit changes are on Sonic Team, not Flynn, but I also gotta be honest and say I'm starting to feel confused on what "Sonic fans" really want from Sonic writing at this point. The original Generations was written by the Happy Tree Friends writers and over time I've been seeing a lot of people say their era of writing for Sonic (which was from Colors up to Forces) is now being viewed more in a negative light as "an era where Sonic went too Marvel and focused too much on humor and not enough on proper character development." Heck IIRC when it comes to Generations I don't think I ever saw people bringing up the story as a strong suit of the original, it was often viewed as "it's there but who cares, I just like that it's actually fun to play." So far I've seen almost nothing but praise for Flynn when it comes to his work on the comics and games like Frontiers.

But the weird part is I also swear back in the late 00s the critique was the exact opposite, people complaining that the plots of games like Shadow the Hedgehog and Sonic 06 took themselves too seriously and the games need to be more silly.

Like I said at the start, it's hard for me to get a grasp on what the "Sonic fanbase" seems to really want out of a writing style for the franchise as a whole.