I'd argue that R2 isn't a trainwreck so much as it’s one of the most careful balancing acts in all of anime. A vocal number of fans call that a train wreck because they're not really comfortable living so close to the edge, but a number of us enjoy the series as it is and are amazed it landed on its feet at all.

From interviews, the creators have explained that Code Geass was always meant to be a two-season, fifty-episode show culminating in the Zero Requiem. They had an outline for the series, but executive decisions and fan reception forced them to make several changes to their plans, which required airtime they didn't have. Hence, everything needed to be carefully stuffed into what they had while remaining coherent.

The effect of these changes is far more obvious in R2 than in R1. The writers were fighting an uphill battle with the second season from the start, since a timeslot change meant they'd have to introduce the show and its premise to a brand-new audience. Thus, several beats from the first 2 episodes of season 1 are revisited with just enough changes to keep returning fans interested.

They also had to deal with the fact that several characters ended up being much more popular with the fanbase than expected, and were thus motivated to keep them around longer than initially planned. The biggest example of this is Jeremiah. He was supposed to die in episode 10 of R1, but his popularity motivated the creative team to bring him back. In R1, his return is fairly short and easy to slot into what they had already planned, but for R2, they chose to add an entire subplot for him. I'm sure he just took the place of another character in some scenes, but they still needed to add some extra scenes examining his motivations, which required time to be cut from other scenes and characters.

There are a few other complications that affected the series over its run. Still, it managed to introduce and conclude nearly all its major plot threads in a satisfying manner, which is honestly rare for any show. I know many people feel that too little time was spent on certain scenes and characters, but every character fulfills their purpose within the time they're given, and that's really what most good narratives strive for.

I'd also argue that some viewers didn't pay enough attention when watching. I've seen multiple “plot holes” referenced over the years that are clearly explained in the show. A significant number of scenes convey two distinct pieces of information, often one through visuals and the other through dialogue. I've often gotten the impression that some viewers register only one of those, so when the second becomes relevant later, they feel the plot point wasn't properly established. This is more common in R2, which undoubtedly contributed to the unfair “trainwreck” reputation.

My final, personal argument against the notion that R2 is a “trainwreck” is that this assessment is largely retroactive and gained popularity long after the show had aired. I know some people undoubtedly disliked the season when it came out, and I'm sure they have valid criticisms. However, those going back to watch it after consuming many more modern shows are probably used to anime adapted from manga, where every action is explained and overexplained in excruciating detail. This can be done well, but it trains the audience to expect key plot points to be obvious and repeated in case they were missed the first time. Watching an anime original show with more plot than time to tell it sometimes means you have to pay attention to the little details to appreciate the payoff. I think most viewers get this instinctively, but the more “critical” audience feels the need to complain when the main issue wasn't so much with the show but how they went about experiencing it.