buying a honda thats only a yr old isnt a bad thing by any means. of course it depends on who the previous owner was, but all in all, there will be no difference than buying new.
did you want an automatic? id try to find a 6spd if i were you, but thats all personal preference.
as far as a warranty, its a good addition that can help you breathe easy, but once again theres not too much you should be worried about unless the person driving it before dogged it. either way you cant go wrong. i personally prefer the 05 design more than the 06.