1. The characters are inconsistent. For starters; In the Cybertron games, Grimlock is fairly based on his G1 appearance. Voiced by Gregg Berger, transforms into a T-Rex, has anger issues, etc; But in Robots in Disguise, he's a black and green klutz who was once a Decepticon and likes working as part of a team. This doesn't add up. Same goes for Sideswipe, who in the games fought during the Great War longer than Bumblebee has. Yet in RID, he's sporting a mohawk and is inexplicably younger and less experienced than Strongarm and Bumblebee. Seriously Hasbro, sort this continuity out. Because it's got more holes than Swiss Cheese.
2. The differing aesthetics makes me wonder if Primus has a short attention span. In the games, all Cybertronians are blocky G1 types with TRON lines. In Transformers Prime, they're heavily based on the movie's aesthetics. Yet in Robots in Disguise, the aesthetics look like something out of Dragon Booster, the Decepticons are all based on Earth animals [not even going to delve into how little sense that makes] and the Autobots are all humanoid. Ish.
3. How long has it been since Transformers Prime ended? I have a hard time believing that Cybertron became a sprawling metropolis after the end of Predacons Rising, yet Bumblebee's arguably become a Prime, Strongarm and Sideswipe are younger than Bumblebee, and human civilisation doesn't seem to have advanced in what I presume to be 50 years. Otherwise, this makes no sense.