Do I really need to say it? Really?
Alice in Wonderland and Peter Pan do have a lot in common (1950s animated features based on classic British novels about little girls from our world being transported to magical lands, most of the same crew working on both, and a few overlapping cast members). This could very well turn into a thesis, so I apologize in advance...
1. Story: Peter Pan wins for this, I admit. Alice in Wonderland is a series of vignettes to the point that I'm almost surprised the individual sequences weren't split up and used as shorts later on (in other words, the opposite of what happened with Pooh). It's one crazy encounter, then another one, and another. None of these have any bearing on each other save for the loose connective tissue of the White Rabbit and, to a lesser extent, the Cheshire Cat. Peter Pan is rather episodic, but there's more cause-and-effect going on. It also has heart, something Alice doesn't have save for a half-heated attempt 3/4 of the way in that doesn't really work ("Very Good Advice"). What's funny is Peter similarly drops its emotional scene around the same time in its story ("Your Mother and Mine"), but the difference is that that sequence is both a payoff to the first third in London as well as a setup for the ending there. The themes of mothers and growing up are more relatable than the theme of a little girl lost in the woods.
2. Characters: Alice in Wonderland. I think a lot of people would agree that what Alice lacks in story, it makes up for in characterization. Sure, there's no character development, but then again, there's no story for the development to even happen in. So while each character is essentially one-note, their minimal screentimes ensure that it doesn't become a problem nor that they will wear out their welcome. They pop in just long enough to make a definite impression, a testament to not only the animators but the talented voice cast. A lot of the characters in Peter Pan don't really get much of a chance to shine. The Lost Boys and the Pirates are each essentially big groups with little differentiating the members of each outside of costuming. If we're to consider Peter Pan the main character, he's a rather self-absorbed one for us to be rooting for. If it's Wendy, while she does have an arc, she's often forgotten about or relegated to the background, so it's harder to us to experience things through her eyes like we do through Alice's.
3. Adaptation: Alice in Wonderland. Funnily enough, of the two, Peter Pan is more faithful to its source in terms of plot mechanics, but I feel Alice is a better representation of its book in terms of tone and detail. Peter Pan is a very whimsical book with a lot of cheekiness to it. The Disney film drops a lot of that in the name of red-blooded adventure. The overall events may be accurate, but the presentation of them is quite different. Because of that, I feel Universal's 2003 live-action film is actually the definitive adaptation of the book (don't stone me!). Alice, on the other hand, may add a lot of its own material and fuses other things together that infuriates Carrollians, but it captures the wit and surrealism of the books well, even if it approaches the humor from a different angle. It also retains much more of the book's dialogue to the point where it's probably the most faithful adaptation Walt Disney Animation Studios has done after The Many Adventures of Winnie the Pooh (which is actually quite literal in places).
4. Songs: Tie. It's difficult for me to compare the two because they have VASTLY different approaches to the musical genre. In Alice, the songs are embedded as part of the dialogue. A character will be speaking, burst out into a stanza or two of song, then continue speaking. Because of that, Alice's songs are quite brief, not to mention numerous (it's the Disney animated film with the most tunes). That means the songs have a hard time finding a life outside the film (only "I'm Late," "The Unbirthday Song," and "Painting the Roses Red" seem to be known by the general public). Peter Pan's songs, meanwhile, are strong both in and out of the film, and all are memorable (though "What Makes the Red Man Red?" does make me cringe...). It has less numbers, but they last longer than the quick blips in Alice, making for a more traditional musical format. Alice, though, has the benefit of having virtually ALL of its characters sing, whereas a lot of Pan's are done by choruses either in the background ("You Can Fly! You Can Fly! You Can Fly!") or by a group of characters who don't get a chance to shine individually ("Following the Leader," "The Elegant Captain Hook"). Both soundtracks essentially cancel each other out for me.
5. Animation: Alice in Wonderland. Peter Pan comes close due some of its cinematography and use of the multiplane camera, but Alice's character animation and background art are more striking. Alice, in my opinion, is probably the most realistically animated Disney character next to Cinderella (Glen Keane studied her a lot when creating Ariel). Wendy, while lovely, doesn't have as much subtlety to her possibly due to her supporting character status. As for the zany characters of each, Alice's have very distinctive acting qualities. They're broad and over the top, yet they don't feel unnatural the way a Don Bluth film does. You can pause the film at any time and find a pose that works on its own in addition to the acting that's going with it in context. Peter's is more serviceable in that regard, with only Tinker Bell and Hook really matching that sense of theatricality. Alice's backgrounds also feel more distinctly Mary Blair with their sleek-yet-kooky designs and patterns. Wonderland feels like its own fantasy world, whereas Never Land often feels like a jungle or forest from ours.
So, in the end, while I love Peter Pan and do feel it has a better story, more heart, and better cinematography, Alice in Wonderland wins for me due to its more memorable characters, wittier script, and more striking animation.
