Which year do you think is the best looking R1? Forget about specifics like color etc... just the overall - function meets form aspect of the bike?
1998-99 - pure function and ground-breaking performance.
2000-01 - further refinement
2002-03 - best function, sharpest lines, most useable power and torque
2004 - the year after Ducati debuted the 999, with the bread-box, underseat exhaust can, fans decried the design and, even though regarded as a better bike, was largely shunned. Yamaha took note and said, "why don't WE do a dual, underseat exhaust?" And so began the weight gain and putting 50% extra exhaust piping up high, where it does nothing to improve handling.
2009 - redesign to return to useable power but still with the excess exhaust piping and weight.
2015 - back to ground-breaking, finally getting rid of the dual, underseat exhaust for better mass-centralization but with a tail that looks copied from the Ducati Panigale, exhibiting the same vent structure first shown in the 1098 in 2007 and continuing into its present form in the Panigale, starting in 2012. I think it has great potential and seems to be the same ground-breaking type of bike the '98 was, I just wish Yamaha would stop taking their cues from Ducati.