There's a ton of little flaws. For instance, logical inconsistencies and absurd plans. Not that that usually bothers me in most things, but since Geass is all about smart people coming up with cool plans, the fact the plans don't make sense often is aggravating. Death Note does that far better, and even it takes some leaps of logic (particularly the anime, as its last arc is extremely rushed).

Another is that the show establishes a semi-harem for the main character, and then does NOTHING INTERESTING with it. Another is some character's motives get unclear, and seem to be walking plot devices more than believable characters.

By going off the rails, I mean that S2's plot gets so rushed and jumbled it's constantly on the verge of not making any sense. At many points, things are just happening, and while you can tell what's happening, you don't really know why. Nothing is foreshadowed or built up to - shit just goes down.

And when important plot points start happening, they feel totally unearned as a result. Like, that important main character died/got mind controlled? Cool, I guess. Lelouch got another absurd upgrade to his army and influence randomly? Fine. That person is actually evil? Whatever, I can believe anything at this point. Which is disappointing, because Season 1's pacing is pretty spot on. They just dropped the ball hard Season 2.

And for that matter, the background story of the magical Geass stuff wasn't anywhere near as fun of a revelation as it should have been. The "rules" of the powers are not as engaging as Death Note (which I keep bringing up, because it pulls off the mind-control concept so much better). Also, a lot of the mecha action and animation is subpar, especially when you could be watching Tengen Toppa Gurren Lagann like a real man.

I know that's a lot of complaints, but I should re-emphasize I had fun with Code Geass, and it had some cool ideas. Just not an all-time anime classic or anything.