To get the ball rolling - I'd sweep out the leadership and pr departments of both Bethesda and Bioware.
Have Bethesda make something set in the near future, with a focus on character, narrative and consequence - bring writing kicking and screaming to the forefront. That and no more gamebryo/creation engine.
Bioware I'd have them try making an surrealist adventure as opposed to yet another party based rpg.
Fallout License goes back to Interplay and a spruced up version of Van Burren gets made.
I'd have id make anything other than yet another fps/tech demo. I'd want to encourage Romero's sentiments of "design is law".
I'd keep the team the same but I'd be fascinated to see what CD Projekt would do with an espionage/stealth game set in 1950's Cold War Europe.
Eidos Montreal. I'm not sure why but I'd be really interested to see what they'd do with the System Shock series.
How about everyone else? How would you like to see developers change?