See Review of Hanlin V5 for V3 owners
for my initial thoughts on the subject. There are now many more font sizes available on both devices (e.g. 9 for ePub), and both run essentially the same software. There is little noticeable speed difference between the two in normal use, which argues for the larger screen device. Transferring ebooks via USB 1.1 on the V3 is slower than on the V5, but ebooks are not large enough for this to be a serious problem.
I have actually switched back to the 6" V3 because it runs OpenInkPot, which I prefer to the standard firmware (although it is certainly good enough to be very usable).