Well, I'll venture to disagree with Ravenus to some degree. I find The Case of Charles Dexter Ward to be slightly flawed, but overall a brilliant performance; it certainly has the most profound sense of "haunted history" of any of his work, though the climactic scene seems a bit too stagey... other than that, this remains one of those for which I have a very high regard. "The Dunwich Horror"... a lot of good there, especially his depiction of the region, the feel of an unnatural history (again), but the simplistic "good-vs-evil" is a bit of a letdown to me, personally (though it remains one of his most popular stories). Still, well worth reading.
As for the ending of "Innsmouth"... the first time I read it, that was my impression too, but on later readings I realized that it was anything but; in fact, it was hinted at from the opening lines, and with a very subtle development throughout the entire tale, and provides the ultimate "punch", if you will, by having not only his physical alteration, but a complete change in his personality take place... he loses his humanity on every level, in the end, so much so as to not even realize that it's a loss... (though it's been argued that it's a gain, really).... It's also a nice touch to have the final lines echoing Psalm 23 (not an original observation on my part; I first ran across it being noted by S. T. Joshi....)