the Rx8 buyers guide is pretty simple as well.
2004-2008 is the series 1
in the US all of the manual trans cars have the high power, or 6 port engine. it uses a 6 speed made by Aisin, its got a bad rap, but on the street seems fine.
the automatic 2004-2005 cars get the low power 4 port engine with a 4 speed, this is a pretty lame combination
2006-2008 get a 6 speed auto and a 6 port engine, and this is quite good

also there were a bunch of updates done for the 2006 cars that were available for the older cars under warranty, but the dealership would have had to know how to read, which means that most didn't get updated.
things like the starter, engine mounts, brake pads, ECU software, etc etc

2009-2011 is the S2. its a bit like the FC, they revised a LOT of stuff
engine gets a completely different oiling and metering pump system, new ecu and cooling system. i'm a little out of the loop, but they seem to have been more reliable
trans is the P type 6 speed, which is like the NC miata. thought to be stronger/more durable.
suspension gets completely revised, different geometry. the 6 speeds get shorter gearing, 4.77 vs 4.44
and it gets new bumpers/lights and interior gets a freshening

 

peejay ain't kidding. The ND is tight, especially the passenger's (right) side. Not much storage in there either.

Even so, we have absolutely love our RF Club. It's been problem free and a blast to drive. Weird how many people notice it too. In my opinion the RF ND and the NA are in a close match of 'which is the 2nd best looking Mazda ever'.