Anime First: The manga that followed can be considered AU, at best
Banned in China: China specifically for: A) Portraying the Chinese leadership as manipulative eunuchs, B) exemplifying the dignity of conquered peoples going hand-in-hand with striking back against the government, and C) having Tibet as an independent nation (reference is made to the Tibet Convention. Something about nudity as well.
Executive Meddling: The original plans for R2 were changed when it was announced that the series would be moved to an earlier, primetime slot. Fans believe that this mainly affected the first half of R2, for the purposes of re-introducing the show to a new audience instead of picking up right after the first season's cliffhanger like the staff had intended. As a general rule, how much a fan thinks was changed is inversely proportionate to said fan's opinion of R2's quality.
It's known that the Time Skip itself was a result of Executive Meddling. Other elements that are commonly suspected or assumed to fall under this include introducing the character of Rolo and removing aspects of C.C.'s and Suzaku's backgrounds without a full explanation.
The level of mecha use seen in R2 may be considered a product of the aforementioned round of meddling, with the show becoming closer to Gundam as a result.
Popularity Redo: The second season was completely reworked because, being very popular, it was moved from the midnight slot to a much more mainstream time, and a lot of the edgy stuff had to be removed. This is arguably the main reason why R2 had such hectic pacing.
Prop Recycling: In R2, Zero often seems to use the same detonator/trigger prop when he wants to make something cool happen.
Reality Subtext: The whole Honorary Britannian thing seems to be taken off from the Honorary White policy applied by Apartheid-era South Africa towards Japanese (and also Koreans and Taiwanese, but not continental Chinese) possibly to avoid South Africa to suffer a trade embargo from both Japan and South Korea, especially in the 1980s when both countries had the quasi-monopoly in advanced electronics and the Apartheid-era government needed that technology badly.
Real-Life Relative: Liam 'O Brien and Amy Kindcaid ('O Brien) are husband and wife, playing Lloyd and Shirley.
In Japanese, Suzaku and Rolo are both Mega Man X. (Suzaku is X-series X and Rolo is Zero-series X.)
Word of Dante: Many fans believe that Lamperouge was Marianne's maiden name, despite the fact that she's only ever referred to as "Marianne vi Britannia", even in media depicting her pre-marriage (such as the novel where a teenage Marianne helps prevent one of Charles' uncles from taking over the throne).