Before we get started, let's confirm the difference between CGI and In-game graphics.
Spoiler:
CGI:
In-Game:
The disappointment is real.
12 years later In-Game:
Better, but still not quite right.
Graphics haven't quite caught up yet. And even if they can handle Perfect Chaos, several things would probably be off, like the water pouring from his mouth in that scene.
Right, anyways what's your favorite?
Mine's definitely Sonic Riders: Zero Gravity's intro.
The robots. The mentioning of GUN. The elevator. The Knuckles gliding in the background which I didn't notice until now.
I'd argue it's all CGI whether pre-rendered or rendered in-engine, but my favorite pre-rendered 3D Sonic Cutscene would have to be the one with the close up of ultra-realistic Perfect Chaos opening an eye.
Granted, I haven't played any of the 3-D games after Heroes, and the 2-1/2 games never made much use of cinematic cut scenes.
Also, pre-rendered is always going to look better until computers become powerful enough to render stuff in real-time that is indistinguishable from real-life by every quanitative and qualitative measure. Not only is pre-rendering almost always done on hardware far superior to the target machine, but it also has the advantage of taking as long as it needs on each frame and then playing back the result in a fraction of the time taken to produce it, while stuff rendered on the fly is limited by how much the hardware can do in a single screen refresh.