Well the ipod comes with everything you need to get it working, including the docking cord (not cradle). This cord plugs directly into the bottom of the ipod and only have firewire and USb2 output. No audio out, like on the dock. So essentually you dont get the fanciness of the stand up dock but it works the same... unless you want to do some cool audio out stuff, then I suggest getting the dock for 39.99$.
The battery issue was pretty much solved months ago. But yes the cost of replacement is 99$ if you dont buy the 59$ Apple care for iPods, which covers the iPod for 3 years.
Well if the iPods are updated soon, then yes the older ones will be discounted.