It's not just the designs' 'toy-friendliness' or lack thereof, but also the fact that the toys are engineered while the robots are still concepts and the designs (including the transformation schemes) haven't been finalised, so that toys can be on shelves before the movie comes out. RotF leader Megatron and DotM Jetwing Optimus are good examples - they're based on early concept art and bear limited resemblance to the final CGI models seen on-screen.

That's also why the RotF versions of Optimus, Starscream and Bumblebee (specifically Battle Blade, Battle Ops/MPM-2, and Human Alliance) look so good - the designers have had two years to study the final CGI models.