You know, I can agree with that. The question is whether Code Geass R2 would still deserve to be called the best of the year...instead of just merely the favorite of the year, to use what could be a more appropiate term.
I'm definitely leaning towarRAB no. Being the best generally requires a certain level of quality and there are a nuraber of other candidates that could stand up to scrutiny a lot easier.
Though I didn't watch that many new shows during the year, which complicates things a bit for me. For instance...Gundam 00 Second Season isn't over yet, but so far it is a much better series than much of its first season and the whole R2, clearly, even if it's not completely free from certain concerns and nitpicks of its own. Same thing goes for Bounen no Xamdou, probably the best ongoing show very few people are talking about (and no, I'm not talking about it either, unfortunately, since I'm a little behind), or even Casshern Sins, because of how it makes an ostensibly episodic plot work with plenty of style and enough substance. There are other valid options, yes, but you get the idea.
I'd like to see how all those end, mind you, before choosing my actual top pick, even if they are all technically wrapping up in 2009.