As part of a Mass Effect retrospective feature in Official Xbox Magazine issue 99, the publication spoke with members of BioWare about concepts that didn't make it into the finished games. While great in theory, non-humanoid party members would have been too costly, it seems.
"Instead, we took all the development effort that we could have put towards an odd squad mate and made a larger, more polished game," said executive producer Casey Hudson. As a result, these characters "had to function like the human characters, be able to carry a gun, etc."
There were also plans to shift the player into different roles that did not pan out. "In Mass Effect 3 we had a moment where the player took on the role of Joker during the Normandy assault," stated senior level designer Dusty Everman.
"Similarly, we'd planned on having the player take on the role of a Quarian scientist before Tali's loyalty quest, and a colonist on Horizon during the Collector attack. It was a bit controversial to not be Shepard, and we thought it better to put the development energy into other places." These games were Shepard's story, so that makes sense. Wouldn't mind seeing experimentation along these lines with the new Mass Effect, though.