Personally, I like both, but for different reasons.
The nunchucks are great for learning flow, and for learning how to control a more flexible weapon. It may be a more "intuitive" weapon, but I would argue that it isn't any easier than your basic stick. With nunchucks, you have to know how to get your weapon back into motion after making contact, how to best move it into position again after you miss, so on and so forth. It takes a bit of practice, but can be pretty easy to pick up. After that, it takes the usual "long time" to master...
Sword is at the core of my heart. There is a beauty and grace about a blade that just can't be beat. As has been mentioned, sword translates easily into stick (single or double), knife, and even empty hand. I personally find the sword to be more meditative, and, at the risk of sounding metaphysical, more of an "alive" weapon. I know plenty of people with swords of all kinds (bokken, practice "beaters", and live blades) that have named their weapons and treat them as old friends/practice partners. I have yet to see anyone do that with nunchaku...
I would recommend that you learn both, but for different reasons. As I said, the nunchucks will teach you flow and redirection, and the flexible weapon experience should not be missed. However, for the meditation, mystique, and general all around applicability, I would recommend the sword.
In any event, have fun with your training!!
Peace--