I just started another play through of MKDA yesterday, due to 20 years from its release, and man, the more time passes and the more MK games out, the more I come to believe that MKDA is the most underrated game in the franchise. As a matter of fact, I believe MKDA is a brilliant game which in many ways was ahead of its time. The reasons why it didn't become more popular imho are that it tried something different, i.e. a fighting game with true martial arts as the backbone of its gameplay, at the expense of blood and gore and flashy special moves, which MK fans had come to expect from the franchise. There is still blood and gore and special moves in the game, of course, but they take a back seat to solid 3D martial arts fighting mechanics and an excellent training/story mode.
MKDA was the closest we had to a tournament viable game until MK9 came around in 2011. It was more balanced than MKD and MKA and various characters had different play styles that required different approaches to using them.
In addition, MKDA had a really good character roster, with a number of good new characters, such as Bo Rai Cho, Kenshi, Hsu Hao, Mavado, etc., and an excellent story.
And finally, MKDA was just so much fun to play. Compared to the latest addition to the franchise, with its awful story, way too many guest characters, unnecessarily gratuitous amounts of blood and gore, and gameplay that is fundamentally not fun (I think the biggest problem with the gameplay in MK11 is that NRS tried so hard to make it feel less like a game and more like a movie, that they succeeded), MKDA is truly a brilliant game.