See, the two examples you gave, are both comedies.
Do you want your Transformers to be comedic? Starscream dropping an avil on Megatron's head? Soundwave pointing Megatron in gun mode at Prime who puts his finger in Megatron's barrel causing him to backfire leaving Soundwave with a blackened face?
Mixing the animation with live action would just look silly.
Besides, in a way, is the CGI style they're using not an animation of sorts?
And I just realised this post could be considered "bashing" OH NOES!1!!1 Though in this forum bashing = simply having a different opinion it seems.