The set and the technical aspects of the show are the biggest reason the quality failed.
Because everyone involved was so busy trying to address all the mechanical problems going on during the run in LA, they did little to no work on the actual show while they were there.
During the big interim between the final performance at The Ahmanson and the start to previews in New York, the design flaws again overshadowed the issues that needed to be addressed with the book and score. At the very end of the pre-production process, Dolly came in with several new songs that replaced the ones that were the biggest problems in LA, but by then the structure of the show was already negated to the point of no return.
The preview period in New York was as underutilized as the one in LA, and the show opened to dismal reviews and disappointing box office returns.
All of that aside, the biggest problem from the project's inception was that there wasn't an effort made to make the theatrical adaptation its own separate entity. As Michael Reidel pointed out, the most successful screen-to-stage musicals have been the ones that have payed homage to the films they're based on while still establishing themselves as a unique experience, which was far from the case with 9 TO 5.
By hiring the film's screenwriter to adapt the book and its star to write the score, the decision was simultaneously made to basically lift the movie and put it on stage. Why would someone pay top ticket prices to watch something they could rent for a few dollars? Had there been bold choices made to set the musical apart as something new and innately theatrical, the success many thought would be inevitable may indeed have happened, but the lack of said decisions is ultimately responsible for the show's commercial failure.
Tonya Pinkins: Then we had a "Lot's Wife" last June that was my personal favorite. I'm still trying to get them to let me sing it at some performance where we get to sing an excerpt that's gone.
Tony Kushner: You can sing it at my funeral.