I have both decks. From an aesthetic standpoint, the Thoth is much more "painterly" in execution; the artwork is often fluid and sinuous. The Magickal's art is much more crisply geometric and hard-edged, more a graphic designer's vision. (On a side note, Anthony Clark's I Ching deck is painterly, so he was after a different effect here.) The symbolism on the Magickal cards is much easier to see and they have more descriptive text. Crowley created much of his own symbolism, drawing from the Golden Dawn tradition, while Clark seems to have built more directly on the GD model, with a nod to some of Crowley's innovations (Adjustment, Lust, Art, Aeon, Universe). This is most notable in the Minor Arcana titles, where Clark retained the "Lord of" terminology that Crowley and Harris dispensed with in the Thoth. Clark acknowledged the Thoth as a direct influence but also went outside it, into the work of Dr. John Dee and also the I Ching. Many of his iconic Major Arcana figures are quite static when compared to the dynamism of the Harris versions.
The Thoth has a better book behind it; although The Magickal Tarot by Tony Willis is quite good in it's own right, it's just not the incomparable Crowley masterpiece (which, of course, you would have to get separately from the deck - but it's a free download). The bottom line for me is, I regularly use the Thoth for reading; I infrequently use the Magickal for study and contemplation. I like both decks, but I find the Thoth much more evocative for practical use.