since i have a 6, i'll speak for it

V6 .:::...
pros
power
better highway speed reaction (i tap on the gas and i fly from 60 - 85mph)
terrific mpgs for a 6 (with my mods listed below, i'm still getting 24mpgs)
comptech support - comptech makes some of the best parts for the Accord, they only work with the V6 platform though (look into the CT IceBox, Supercharger, and Exhaust)

cons
SOME transmission issues (people paint a picture like every tranny put into a 6th gen breaks ... the actual rate is at 2%)
auto only

if this car is going to be a highway commuter car, go for the 6.