We actually have both. Our bunks are a twin on top, with a full-size underneath (yes, they come apart), and we invested in a trundle for underneath the bottom bunk.
I did this so there would be minimal arguing. One gets the cool factor of having the top bunk, the other gets the bigger bed. I also like having the bigger bunk underneath, so when we have more than one kid sleep over, two people can sleep in the lower bunk.
We never actually got around to building the trundle drawer, and just keep the mattress shoved under the bed. It's much easier to slide out - you can slip it sideways and drag it out at an angle, vs. having to move ladder and furniture to pull a big drawer out.
I ESPECIALLY LOVE having the trundle in there with them, so that when one or both are sick (as was the case, last week), I just pull it out and sleep in there, rather than trudging back and forth across the house all night.