I have only been to Sea World, Orlando, two times. The first time, we just wandered around, aimlessly, learning the layout of the park. Journey to Atlantis was down that day.
The next day, we were there at opening, and went straight to Journey to Atlantis. We rode it three times in a row, with no wait (maybe five minutes). We could have kept going, but we wanted to see more of the park. Our next trip, I will keep going and going and going on Journey to Atlantis. We just got tickets, for $25.00 each, read one of the other posts, so we are planning one day to Sea World in December. I cannot wait to ride Journey to Atlantis again, again, again, again, again . . . . Our DS, however, will be tall enough to ride Krakken, so I may have to wait for him over there, too. I will not ride Krakken - motion sickness - I know, call me a wimp.
Journey to Atlantis is in my top ten favorite Orlando attractions. I loved it. I also love Splash Mountain, which is also in my top ten favorite Orlando attractions.
I love the music in Splash Mountain. The story in Atlantis is cool, too; but I would give the edge in sound to Splash Mountain, but just an edge.
The theming of the que line in Splash Mountain is much better, but who really wants to spend much time in the que line. Journey to Atlantis wins in this category, at least when we were there - August - since I totally enjoyed the five minute or less wait in the que line. I assume the que line can get long at Journey to Atlantis, so do not rely on me for this. I can only tell you what it was like one day in August 2006.
The theming of the rides is about equal, both are great. Both could use a touch of paint, here and there, but that is about it. I absolutely, totally, without question, love them both. Afterall, Orlando is about attractions, and these are two of the best of the best of the best.
Finally, there is the thrill factor. Journey to Atlantis wins in this category. The roller coaster part is cool. The drop is about the same in both. I think you get a little wetter at Journey to Atlantis; but I usually avoid the front seat of Splash Mountain.
To me it is just like Splash Mountain, but with a different theme.
Enjoy.