<< Is there a significant advantage to the Nalgene bottle and cup? >>
Beats me - I go back and forth. My pendulum is about swung back to canteen and cup, though.
As for spilling when filling from cup-to-canteen - it's a wash. The surplus canteen cup pours very accurately and I've never felt sloppy or handicapped with filling a canteen that way. The Nalgene wide mouths are a bigger target but the cups that fit are not as accurate to pour from.
I much prefer using the canteen cup for heating/cooking/eating/drinking from vs the nalgene cup. Nalgene cup is lighter, of course. Canteen is better for me to drink from, as well. In sub-freezing weather, I prefer the widemouth Nalgene over the standard canteen and I prefer it over canteens for "bulk" water.
I guess it mostly depends on what I'm carrying and what role the canteen/wide-mouth Nalgene serves in my water lugging scheme. Both systems have good points now that there are widely available "nalgene cups".
Regards,
Tom