As a huge Zappa fan in HS, I was also by law a huge Captain fan. I think the reason why his stuff gets more cred than Zappa's is because it seems to come from a more real, less calculated place. As strange as his music and lyrics were, there's something undeniably organic about them.
I had that same experience listening to "Trout Mask Replica" that nearly everyone has. The first time I heard it, I admired its ambition but couldn't get into it. Then I gave it another shot and it grew on me a little. And in the next listen it grew on me some more, until finally I realized how amazing it was.
We won't get another one like him. I'm not sure we got the first one.