1, The outrageous Japanese wet dream premise. This takes a bit of background explanation but basically the Japanese feel really
really sorry for themselves over the end of WW2 and want everyone else to do so too.
2, The mess that battles eventually turned into. The conceit that Lelouch, a high school student, was the only person capable of micromanaging his army and that they were really fucked without him (See the end of S1). Real battles don't work anything like chess, and aren't won by having a great idea or two about how to use the scenery to your advantage. It had the effect of artificially dumbing down all his opponents, and I can't stand that.
3, The hamfisted racism theme. Japan can't into discrimination. They just can't. Whenever Japan does discrimination it comes out smelling awful.
4, The pacing and energy of the series meant that the plot didn't slow down for new characters introduced, which left them kind of hanging there until they were useful and then having a few odd lines. The biggest offender being Rakshata, but there were other characters who didn't bring anything to the story and had no characterization.
5, The plot twists. The
you know what in S1 that was basically the equivalent of prolonging the series for thirty episodes by slipping on some banana peel, and the philosophy that
every single episode in R2 needed to end on a cliffhanger. Suddenly we're back on the level of movie serials to hold the viewer's interest. Special mention goes to the Black Knights betraying Lelouch towards the end of R2. I mean, haha what?
6, Overuse of amnesiurrrrgh. It's fine when Lelouch's power can cause it and Charles' power does cause it, but when a character independently gets it herself, it's overusing maybe the most hackneyed dramatic device in the book. Special points go to Geass inflicted amnesia and 'real' amnesia happening within the space of two episodes.
7, The two times Lelouch won a conflict by predicting everything his opponent was going to say within a five minute conversation. You fucking what?
There are other more minor things. It's a very very fun series. Always entertaining, but I wouldn't call it well written. It's junk food like pizza (How apt!)
Oh shit I forgot a big one. The fact characters don't die unless you explicitly see them bleed out and pronounced dead on camera, otherwise they come back in increasingly stupid ways.
This later becomes a habit of the main writer.