Usually a newer edition is something that at least the author and publisher considered an improvement, so any answers are rather subjective. That said,
Ian Stewart's Galois Theory, 3rd edition, is sometimes harshly criticized for ruining a great book, by (1) doing everything over the complex numbers first (leading to some long-winded proofs), and (2) being full of typos. The former is a conscious choice of the author, so its merits are debatable, but at any rate it's a substantially different book from the 2nd edition.
Calculus Made Easy, by Silvanus P. Thompson. This 1910 classic was updated in 1998 by Martin Gardner, but because both the authors are "men of strong individuality", the difference in styles can be somewhat jarring. Also, John Baez complains that:
Alas, the new edition has been puffed up to 336 pages by Martin Gardener. People must want calculus to seem hard.
