Its mostly personal preference. With standups you can see over the bike easier, and I tend to get more wobbles with sitdowns.

 

Standups are alot easier to pull up. Like squidmark said its personal preference, but i can feel balance point alot better in a standup position. You can also control balance point with your body when your standing (hanging off the bike more lowers BP). And when your doing a sitdown by the time your in balance point you wont be alble to see anything but gas tank infront of you.

 

Stand ups just feel good to me. You can move around more, steer them easier, play with the bp more. There no better feeling in the world when you can keep them up for miles. I would definitly recommend to be comfortable with sit downs first. Once you get used to them stand ups are easy. The main thing is you can see everything when your up there.