As someone who played Mortal Kombat Vs. DC Universe, I feel this game gets too much of a bad rap, especially when compared to later MK games like Mortal Kombat 2011 or Mortal Kombat X.
It is true that the gore is toned down, but that was mainly because of the DC Comics license. As DC Comics had restricted Midway (now Netherealm Studios) from being too graphic, the trademark gore is toned down to the point where the game is Teen rated, which angered a lot of MK fans. Also, while the Mortal Kombat and DC Villains were allowed to have Fatalities, the DC Superheroes had to have a new finishing move called "Heroic Brutalities" because DC Comics said Superman and Batman do not kill.
While that basically subtracts points in a franchise standpoint, it however does not detract from the gameplay. The game is basically a 3D fighter like Deadly Alliance, Deception, and Armageddon before it, but it does change the mechanics up. Gone are the ability to switch between fighting styles and the Kreate-A-Fatality mess that ruined Armageddon to me, and instead, we get new mechanics like Free-Fall Kombat, which allow you to pummel your opponent to fill a super meter, with the opponent also has a chance to block an attack and turn it around in his/her favor, and Klose Kombat, which does a close-up of the two fighters and whoever did a grapple would start attacking the opponent until a certain amount of hit or the fighter being attacked manages to match the attacker's button press, allowing him to dodge and end the Klose Kombat with a Kounter Hit. There is also a two-gauge that fills up as you take damage, with one allowing you to perform a Breaker as seen in Deception and Armageddon, while a full meter activates Rage Mode, in which the fighter goes into a Kombat Rage that makes him/her do more damage and be immune to being launched for a short time.
And instead of a Konquest mode, we get a Story Mode which explains the events of the game and why these two properties are fighting with other. It has two different sides of the story, the MK side and the DC side, each showing different sides of the conflict. However, the one thing harming this mode is that it's pretty much straight forward: just beat the opponent to move on.
Another thing that can also hold this game down is some of the finishing moves. As I mentioned earlier, the DC license basically forced the game to be toned down to the Teen rating. While they do return some classic Fatalities in good form(like Scorpion's famous Toasty fatality, which just burns the opponent until his/her body is completely black, as well as Liu Kang's arcade machine drop from MK3, complete with the MK1 arcade machine, even though it does not crush the opponent to a bloody mess), some have not been done well, and new Fatalities that do look bad (like Jax's Head Clap causing the opponent's head to be flattened in a Looney Tunes-like fashion, and one of Kano's fatalities has him just jump on his opponent's chest like he thinks he's Goro). Also, the Heroic Brutalities are a good way to keep the DC superheroes in character, but some of them basically look like actual Fatalities (especially Green Lantern and his energy sphere of bone-crushing death).
Despite these problems, Mortal Kombat Vs. DC Universe is still a good game, and while it was the final game made by Midway before the company went bankrupt, Ed Boon and the rest of the MK team would be acquired by Warner Bros, and move on to make Mortal Kombat 2011, which would return the series to its roots, and Injustice, an all-DC fighting game that would have Mortal Kombat fighters as part of the DLC roster.
