Or you can skip the whole ride and enter the exhibit through the exit. I'm not a big fan of the ride, but the exhibit is phenomenal! But if it's your first time in the park, go on the ride and see for yourself!
As for the Haunted Lighthouse, I was told that it was changed to a Sesame Street themed "4-D" movie. It's definitely for kids, so it may not be entertaining unless you still love Sesame Street.
I assume you are talking about Sea World San Diegio, not Orlando or Texas.
I was actually just there. The Shamu show is basically a must. Atlantis is okay... what you see is what you get, there are no real additional surprises. If it looks fun when you see it, then go for it. I like it, but not love it, and definitely wouldn't wait a long time for it (20 minutes max). Shipwreck Rapids is a standard rapids ride, with some pretty good theming. If you ride it, keep in mind you will get drenched.
I personally think the ride simulator part of Wild Arctic is terrible. I usually do the "go straight to the exhibit" line. The exhibit is fantastic, just not the motion simulator beforehand. Penguins are great, of course. Sky ride and Sky Cabin are nice, but upcharged ($3 each, or $5 if you decided to ride both).
I would definitely go through the Shipwreck Cafe, even if you don't intend to eat there. The theming is great, there are animals and fish around, and you can see many sections of the rapids ride you can't see from the rest of the park.
The 4D movie is no longer R.L. Stine Haunted Lighthouse (thank goodness... I hated that film). It is now a 4D Sesame Street movie. Cute, and if you like Sesame Street, go for it. There is also the new Sesame Street Bay of Play, which has a few rides: a Dumbo-esque ride, a Rockin' Tug, and a Teacups style ride.
Do take your time walking around... the landscaping is beautiful, and most of the exhibits are all pretty good.