Moria calls it "the best of the 1960s Godzilla sequels." Slant Magazine says, "it's through this simple morality play that Ghidorah accrues much of its charm—not to mention its delirious wrestling match antics." 1,000 Misspent Hours opens with this:
It’s well known that Ghidrah, the Three-Headed Monster/... marks a major turning point in the history of the Godzilla series. This, after all, is the movie in which Godzilla first becomes a good guy. But Ghidrah marks the beginning of a new era in other ways, too. Most noticeably, it is here that we see the first appearance in the series of the sort of wildly imaginative monster designs for which the Japanese would later become famous.
Million Monkey Theater says,
There are two camps--those who find this film a true classic of the original Godzilla series, and those who absolutely loathe it as being the beginning of the end for the evil antagonistic Godzilla we had all come to know and love.
The New York Times closes by saying,
This fascination, on the part of contemporary Japanese film makers, with the destruction of their land by fantastic, prehistoric forces only 20 years after Hiroshima, might be of interest to social historians. The film, otherwise, is strictly for the comic book set.
WTF Film has a recent long post that concludes:
This is a Godzilla movie that’s got a little something for everybody. It’s a monster movie, it’s an action film, it’s an adventure film, it’s a spy film, it’s a movie about coming togetherness. And no matter how you like your Godzilla—mean and serious or funny and heroic—he’s here for you. If you haven’t seen this one, what are you doing reading this? Go out there and grab it!