Lack of success due to McDD running out of money and starving the project of R&D funds (notably on the aerodynamics side). So it was a pile of poo done on the cheap.
Same thing afflicted the other McDD aircraft of the 1990s, the MD-11, which you will notice has similarly vanished from mainstream passenger operators.
The MD-90 was the ultimate overstretch of the DC-9 with lots of elements (starting with a 5-across fuselage) unchanged from 30 years beforehand, while others advanced.
Final straw was the arrival of Harry Stonecipher at McDD as president, who killed the future of the company with poor management tactics all round. The only significant sale made after his arrival was to Saudia, which was done at government level.
Some MD-90s have been scrapped with less than 10 years service.
Boeing sensibly didn't continue it. It's lack of market appeal was apparent on the day of the merger.