I'm just going to say since I know where this is going :P You hook the power cord to the cradle. So now when you want to charge it you just lay it down in the cradle instead of trying to plug it in all the time.
Sure it sounds almost a no point but OMG it makes a world of difference..... that is til i got the power pak+ and my enjoyment crashes down on me.
It's just more of a convenience when you need to charge your 3DS. Instead of plugging in the charger directly to the 3DS, you just lay your console on the cradle to charge. However, I find the charge cradle to be very useful. I can't play my 3DS without having the cradle attached, the system is just too small and thin for my liking.
It seemed kinda pointless to me too but I set it up anyway since it was there... It's actually pretty handy since I just keep it on my table next to my couch and just plop my 3DS down on it whenever it needs to charge. Helps to clear a designated spot to place it, and cuts the minor hassle of having to plug/unplug the cable all the time.
Dunno... You pretty much just have to figure out what to do with it on your own I guess.