We got bunk beds for my 2nd and 3rd sons when we found out we were expecting #4, and honestly, I HATED them. They are a big pain in the butt when it comes to changing the sheets, especially if the bunk bed has one side against the wall. I had to climb up into the top bunk and try to get the mattress pad and fitted sheet on, then try to get the flat sheet and comforter lined up while doing a balancing act on the ladder.
The bottom bunk wasn't really any easier because I would almost always wind up bumping my head when changing the sheets.
It also, surprisingly, to me made the room feel smaller because it was so tall, it was almost like a wall that visually shrunk the room.
The boys had a love/hate thing going with the bunks- loved it during the day, usually hated- or at least disliked it- at night.
At any rate, we wound up separating the bunks, and even though it takes up more floor space, it actually made everyone happier. I would say if you do get bunks, make sure you get the kind that can be separated, so at least you have options.
If I were in your shoes, I'd put them in separate rooms. I think when kids have their own space they can go to, they are more likely to get along. My brother and I each had our own rooms when we were kids, and when we would get mad at eachother, we would go into our rooms and slam the door. After a little time apart, doing our own thing, we'd cool off and be friends again. I can't imagine what it would have been like if we couldn't get away from eachother for a while. Ugly- lol.
Best wishes with whatever you decide :)