Fed was gash in Miami. He was average in Rome and Basel also (he was OK, but fairly slow/pale, in AO '08 - regardless, Nole played a great match). USO '11 was definitely higher quality than in '10 - Fed looked supreme in those first 2 sets. Fed was also better in AO '11 than half the ones mentioned, though he did severely mess-up his second set lead.
I'd actually say one of the best matches between the two is in Toronto 2010 SFs - Fed in godmode for a set and a half, Nole fighting back in the second going for every shot, and a tense decider 7-5 to Fed (after leading 4-1 iirc and saving BPs at 5-5). Obviously RG last year was consistently high quality also.
As for YE #1, going to be very close. I think Djokovic edges it, but it really is going to come down to what he makes up in the indoor season and what Fed manages to defend.