According to "The Annotated Huckleberry Finn" by Mark Twain and Michael Patrick Hearn, Twain was already having a hard time wanting to do another "boy book." He had been working on suggestions made by friends on how the last part of Tom Sawyer should serve as sort of a prequel to the beginning of Huckleberry Finn. In the end, according to Twain himself, he was just tired of it, even quoting:
I like it tolerably well and may possibly pigeonhole or burn the manuscript when its done
Instead, he abided by his premise that "books write themselves" and, instead of burning it, he worked on other projects and did not pick up the book again for SIX years.