Note: I don't think there are many spoilers in the following, though there are "meta-spoilers" -- concepts that become apparent after one watches these films. If you don't want your thought-space cluttered and you intend to see these films, you may want to skip this post.
Both movies are actually pretty good, which is to say, entertaining. "The Illusionist" has a fairy tale quality and the merits of simplicity; its dominant metaphor is the illusionary quality of cinema. "The Prestige" is more complex and discursive; it's ruled by the metaphor of electricity -- which is to say, invisible power. Christopher Nolan's film gives a critic much more to chew on, both in terms of its myriad plot twists and concealments, and in terms of the self-reflexivity of its dialogue. "The Prestige" is the kind of film Slavoj Zizek would enjoy, while "The Illusionist" is the kind of film Sigmund Freud would enjoy.
In magic, the magician is like a therapist. The audience comes to him to be told that there is in fact still mystery in the world, or at least technical skill so good it passes for mystery. (Even if everyone in the audience knows it's a trick, a sense of mystery attaches itself to the magician, the performer, who makes the sleight-of-hand seem believable.) This is therapeutic because "we" want to believe in the existence of mysteries, or at least we did at one point in the recent past (modernity). The magician is like a priest, who trades not so much on his audience's faith but on his audience's desire -- even unconscious desire -- that the trick be "real."
These metaphors are the films' subjects. The two films are actually quite different when it comes to how they frame the performance of magic. "The Illusionist" aligns itself with the magician-hero, and amplifies the mystery of Edward Norton's invocation of ghosts--before deflating the mystery at the end. "The Prestige," on the other hand, proceeds by indirection (like a magician itself), and gives many indications along the way that its purpose is to show the work "behind the scenes" of magic. The disappearing bird trick is explained, and it turns out to be ghastly: when the magician waves a sheet and then puts his hand down on a flat table where, moments before, a live bird fluttered, he has actually collapsed the cage into the table and killed the bird. The bird that appears, "magically," in his hand a moment later, is in fact an identical bird, his "brother," as a distraught child says at one point. The bird becomes a sacrifice -- something the magician must destroy to give his audience the illusion it wants. By showing us the trick, the film distances itself from from the performance, which "The Illusionist" avoids doing. But as the ending of "The Prestige" is approached (and I won't give it away), the film reverses itself, and comes to embrace the aura of "magic" it had earlier been debunking, and it does so, surprisingly, using the idiom of science itself -- Nikola Tesla in his latter years.
Which brings us to the present moment, which it might be convenient to call "postmodernity." Now we happily use IMac's and drive fancy GPS enabled cars (note: not me), and have only the faintest idea of how they work. We might know the components, but we have neither the technical capability nor any particular interest in knowing how the machines around us are engineered. We're in a bubble of technical illusions, but we have little to no sense of "mystery" as a result. If in modernity electricity was mysterious ("invisible power"), in postmodernity the functions and devices it enables are merely there. We could extend this to the films themselves, or more specifically the gap between the films' subjects and the films as we experience them at the present moment: the magicians are mystifiers in modernity (who seem to want to resist it, but in fact depend on it entirely -- cinema, electricity), but films about modern magicians are mystifiers in postmodernity. They show us illusions of illusion, and we still want (unconsciously, perhaps) to believe they're real, or at least, "real."