These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Sonic's model suffers from an incredibly bizarre design choice for long, rigid spike-length hairs and a very oddly placed, sized and animated mouth.
The computer generated imagery in general. There are plenty of models and surfaces that are well designed and rendered (the Gamma robots come to mind) but various elements - such as lighting◊ - of live-actions shots are not accounted for in many CG image renders. In addition, many CG elements have no physical bearing on the environments they very obviously interact with in many shots. Numerous shots of CG elements generating no disturbance on a forest floor with thick leaf cover are prime examples.
Uncanny Valley: Sonic's appearance is pretty much lifted straight from the games, with the only real addition to his design being making him actually look vaguely like he has fur and spikes akin to a real hedgehog. This, combined with the Darker and Edgier setting and placing him alongside live-action humans has... not been to everyone's tastes. A similar scenario happened with Sonic the Hedgehog (2006) in attempting to render humans, Eggman/Robotnik included, realistically, whilst keeping the cartoon animals the same. By the next game the humans were reverted to looking more cartoony as a result of the negative effect.