If you're an aggressive person capable of controlling your own destiny and room, take the bottom. You can keep people from using your bed as a seat by force of will. Meanwhile it's more convenient. You can use the bottom bunk as a seat, it's easier to fall into and out of while sleepy, and the storage space underneath it is defaults to you (even if you split it, it's simply more convenient for you).
If you're a passive person who like to avoide confrontation, take the top bunk. You can use it to retreat away from others. And if you're pretending to sleep, no on really can say otherwise unless they're willing to climb up and into the bunk with you. The ceiling becomes yours by default... so you can put post-it notes, posters, or those annoying glow-in-the-dark stickers up there. The top bunk is largely un molested by strangers and other people, so you can actually make your bed and keep it the way you like.