The Arduino uses Wiring which is an implementation of Processing which is Java, if you're comfortable with object oriented programming there's not much to learn except syntax. The NetDuino just changes the development language to C#, if that works for you then fine but you'll lose a massive network of support as far as program debugging and tips goes for Arduino native projects.
Unless there is some truly driving need for your to use C# then I'd recommend Arduino, neither platform is inherently better which is why you'd chose the Arduino, with nothing being better or worse it's a matter of taste and with the support for Arduino directly you'd need a REALLY good reason to use the .net framework.
I can't think of one advantage the Netduino project has over Arduino, and the lack of community support as strong as the Arduino has is a big tipping of the hat in it's favor.