Why are tandem pedals mounted with the same position?
Sheldon goes into some detail on this.

Having the pedals 180&deg; out of sync would lead to a couple of problems: 


Starting off, as most people have one foot on the pedal and lean towards the other foot on the ground, including both people on a tandem.
Foot overlap.  There's often not enough room for the captain's foot to be at the back of the stroke and the stoker's to be at the front without them colliding.
You couldn't corner with the outside foot down, as the other person would have the inside foot down and strike the ground.


A phase difference of 90&deg; is used sometimes.  The power is more even through the stroke but handling is worse at low speeds among other downsides.

Another post dicusses 90&deg; out of phase and also slightly out of phase

The second article suggests that most people ride exactly in phase because that's how tandems are set up by default.  Changing takes some getting used to and a little fiddling so people need a good reason to mess with it.