...my personal theory that Zephram Cochrane had nothing to do with warp drive.
That rather, it was LILY who invented the warp drive and Zephram and was just a test pilot that Lily hired...
Ah, but Zephram Cochrane didn't even like to fly; he took trains.
"You think I wanna see the stars? I don't even like to fly! I take trains!" -Zephram Cochrane
I think Lily and Zephram were both engineers/physicists. Lily was probably just as qualified to pilot the thing as Cochrane, but let him/forced him to take the front seat because the invention was based on his ideas and technology.