It appears that most later critics think that Twain's criticism was unfair, and possibly intended as humor.
John McWilliams writes:
Hilarious though Twain's essay is, it is valid only within its own
narrow and sometimes misapplied criteria.1
Some other sources cited by Wikipedia appear to claim that the essay was not intended as a criticism at all, but as humor, because Twain's criticisms are not realistic. In this essay, Twain is "Impos[ing] the standards of Realism on Romance," which is humorously incongruous.2
1 "Fenimore Cooper's Literary Offenses (Introduction)". Twain's Indians. University of Virginia.
2 Andriano, Joeseph. The Routledge Encyclopedia of Mark Twain p. 287 (1993)