Bioware gets quite a few things wrong nowadays but I can't agree with this being one of them. I thought it was a welcome shake up to the gameplay and functioned perfectly well. To ease players into this system over 3 or 4 chapters would of been of a waste of time and bloated story. It's such a simple piece of gameplay, it takes all of 5 seconds to understand.
I do agree with the OP thought. I would like to return to the Republic vs Empire, actual Star Wars.