I personally really enjoy the Real-D 3D, but it does take some getting used to. You have to realize that the images you're looking at have depth, so your eyes have to work a bit more because what you're looking at has depth just like a real image. You can't just stare at the 2-D flat screen.
I think Prometheus wouldn't be a bad movie to experience 3D in for the first time. From what it sounds like, it runs at a bit slower pace and has some very nice visuals and wide shots. This would be better than seeing something with tons of action and super-fast FX scenes or complicated shots.
I watched Wrath of the Titans in 3D, and it was amazing, but some parts were so fast it could make you dizzy. There were also constant explosions and things like that, so I was flinching because it looks likes things are flying at you.