That's exactly how I felt when I finally got to ride the subs at Disneyland last year.
When I was a kid we came to WDW several times, always during Oct, and it was always drained. I have some great pics from the Skyway, though. I grew up with this big feeling that I had missed out - because not only do I love dark rides, I also thought it was amazing since it was really underwater.
When I finally got to ride them in Disneyland, as I said, I felt exactly as you said. It's gorgeous looking at, I loved standing near the lagoon and just watching the subs go through. However, the actual attraction is kind of uncomfortable, sitting hunched over trying to see out the tiny viewports. It was neat, but it wasn't some amazing thing.
That's why, personally, I think we got the better version of Nemo. We get to sit in comfortable omnimover seats, see basically the same story and effects save actually being underwater, and at the end we get to see a massive water tank with real animals in it. I also couldn't help but feel bad how inaccessible the subs at Disneyland are - no one with any mobility issues whatsoever is able to experience that attraction.
It certainly is neat, but I lost that "wow I missed out when I was a kid" feeling once I actually rode it and sat hunched over a few times.