In the end, Russ Cargill was the right choice for the main villain, because he’s barely a villain. He doesn’t interact with the Simpson family much, and when he does get to talk face-to-face with Homer and Bart, he’s killed in an absurdly anti-climactic way by Maggie. (Admittedly, Maggie’s been well-established as a potential murderer by this point, so it’s not completely out of nowhere.)
Cargill serves his purpose as the shifty government official who moves the plot forward in the final two acts, but for the most part, he just hangs back and lets Homer’s internal conflicts take up the movie’s focus. This was a smart screenwriting choice, as it allows the movie to give Homer what might be his best, most substantial character arc in the show’s 30+ year history. As some fans have pointed out, “The Simpsons Movie” basically serves as the end of the Jerkass Homer trend. At the start of the film, Homer is at his most selfish and cruel, but this time he properly atones for his sins. Throughout the rest of the show, Homer’s a nicer, tamer character than he was throughout the early 2000s.
It’s a decision that makes “The Simpsons Movie” feel like a meaningful part of the show’s history, as it’s actually had a (subtle, but substantial) impact on the way its main character is written. It’s a decision that would’ve been hampered if they decided to let Hank Scorpio take up too much of the spotlight. Hank didn’t get to be in “The Simpsons Movie,” but as great a character as he is, he simply wouldn’t have belonged.