I'd chalk it up as a plot conveyance to keep him from being egotistical and antagonistic. I don't think he was really in the Casey Jones role, so much as they needed another human character. It's disappointing though that an actor that's famous for jerky, nasty, egotistical characters that wind up making themselves look like fools got a character who in his original form
was a jerky, nasty, egotistical character that winds up making himself look like a fool didn't get to play
that version of the character.
But it is easier to overlook keeping Eric Sacks in the movie for the sake of the actor. My number 1 complaint right there. Seems if the film didn't cave into complaints about Shredder not being Japanese that close to production, it wouldn't have felt so disjointed right there.
There's something else that bothers me about Baxter in the 80s cartoon series: if they were going to have Pat Fraley do his voice, why didn't he give Baxter a voice other than one that was almost virtually identical to Krang?
I never liked pre-Fly Baxter in the cartoon anyway. The geeky scientist type from the 1980's that was all based off of Jerry Lewis... yeah. I really hated how that's how Baxter was played, partially in retrospect of the comics and newer cartoon shows. Too subservient and the Coconuts to Bebop and Rocksteady's Scratch and Grounder in terms of Shredder's abuse. But a real milquetoast. Then he turns into a fly and becomes vengeful and crazy, and that improved on the weak character they used.
Comic and cartoon Baxter was always more egotistical, thinking he was the greatest genius of all time for his inventions. I'd say Baxter was the
best villain in the 2k3 series, and a highlight of that version overall. His outwardly Starscreamish personality was tempered by the fact that he got into science because his mother wanted him to help others and was so darn proud of him. He even got that amazing banned episode you had to buy a DVD to watch. I do like this series iteration of Baxter, trying to cross the two. Especially since the other villain mutants abuse the crap out of him. Not so much as Hun did last series, but just enough that you know that he's planning something, and then gets smacked down back to a subservient role.