Once Christopher McQuarrie came aboard to handle rewrites, that’s when a good portion of Mission: Impossible – Ghost Protocol, primarily the latter half, was changed.
Brandt came back for Rogue Nation, but because Jeremy Renner was busy in the Marvel Cinematic Universe, he didn’t return for Fallout.
He was introduced in Ghost Protocol, and with movies like The Hurt Locker and The Town on his resume, it’s easy to see how the creative minds could have envisioned his character as a worthy successor.
As for who this agent was supposed to take over Ethan’s spot as the main action hero, my guess it was Jeremy Renner’s William Brandt.