Musically, it's entirely different from anything else. and I thought that it was a place, an opportunity, to begin a love song. I remember Brian pressing me about the relationship between the mother and the father and the child. And this is the guy who wrote "When I Grow Up (To Be A Man)", the guy who is becoming a man. I really think that he was thinking about his own personal progression from childhood. Now I thought, once we had gotten "Heroes And Villains" done, we might have seen a boy/girl song emerge, other than "Wonderful". Honestly, I really thought we would do it, but I never found an opportunity to pursue that with the music I was given.
Author Andrew Hickey described its lyrics to be the story of a girl devoted to God and her parents who is thrown into emotional disarray after encountering a member of the opposite sex. Biographer Mark Dillon interpreted the song as the story of a young woman and her steadfast embrace of adolescence through the loss of her own virginity. He continues to describe the original version of the recording as "proto-psychedelic chamber pop".
When it was remade for Smiley Smile, one verse was omitted from its lyrics, it being replaced by a 35-second interlude described as "a left turn into a hash den" by Dillon. Containing the group's giggling and nonsense doo-wop chanting, the phrase "don't think you're God" can be heard in the mass of voices. Dillon suggested that this interlude represents the female protagonist's sexual awakening.
Author Andrew Hickey wrote of the song, "If there was any justice in the world, this song would now be regarded as every bit the classic that "God Only Knows" is, as on every level that matters – musical and lyrical sophistication, beauty, the compassion that pours out of every syllable of the song – this is the superior of that song and almost every other I've heard." In 2011 Mike Love commended Parks' "marvelous job" with the lyrics and has described the piece as beautiful and sensitive, possessing ability to move listeners to tears. He told Goldmine magazine "‘Wonderful’ is an amazing, amazing piece of work. Holy shit! Van Dyke and Brian did a great collaboration on that one. It’s a really beautiful song. That’s probably my favorite thing from the Smile project.”Power pop musician Matthew Sweet praised the Smile version for its baroque feel, whereas "it gets a little more trivialized on Smiley Smile".
As a solo artist, Brian Wilson revisited the song in 1995 for his I Just Wasn't Made For These Times album, and then again for Brian Wilson Presents Smile in 2004. The latter version was released as a limited 7" single backed with "Wind Chimes" totaling 5,000 copies on blue, green, and yellow vinyl. In the 2004 version, "Wonderful" is linked thematically with the second suite which also included "Child Is Father of the Man" and "Surf's Up".