My line of thinking is that Megs was only disliking of Organics with Beast Machines, as he seemed to actively enjoy both of his T-Rex & Dragon forms; Only with the advent of Beast Machines throwing out 3 Seasons worth of narrative did he begin to "Hate" organics - At least that's what I thought.

It's an interesting question as to why he ended up more of an Organic Dragon (Not that I'm complaining, the toy is beautiful).
Perhaps it could be based more so on what is at the "Laser-core" of a particular Spark and hence manifesting itself accordingly?

Original Megatron was a maniacal dictator, bent on the conquest of the Universe whereas Prime was a leader who's own spark had been heavily influenced/mutated by those that had previously held the Matrix.
Maybe because of these influences "Evil" manifests itself as a Beast & "Good" the form of a/the divine being, as this particular being is Primus and all Cybertronians are supposedly made in his image (Transforming Anthropomorphic Vehicles, initially), the end result is far more Vehicular/Mechanical in nature?