Double deck might be possible, however, one level would have be be as low to the ground as possible, and each level would have to be only about 6 feet floor to ceiling. It would be impossible to any kind of room for strollers and wheelchairs. Also, it still might not work through some of the tunnels.
Probably not a good idea.
Here's the inside of a Metra Train in Chicago that is double deck:
Link