The point here is, you cannot compare character storyline, overall game storyline, character designs, between two different references, and still say you are comparing video games. It then becomes something entirely different, as in "Which Mortal Kombat game did you LIKE more than the others." Like, enjoy, prefer, etc, have nothing to do with a game being good, because the words, "good", "better", and "best" have nothing to do with "opinion." When someone says "I liked MK1 the best" they are using the term "the best" incorrectly. Best implies measurable and quantifiable limitation.
http://dictionary.reference.com/search?q=opinion&x=0&y=0
http://dictionary.reference.com/search?q=best&x=0&y=0
As you can see, it is possible for them to be completely unrelated.
When you compare games, you have to look at the gameplay first and foremost. It's the only measurable aspect of the game. Gameplay includes:
Character Count. The more characters in a game, the more chance there is for variety. More does not always present variety however.
On the fly options. Not gameplay modes or difficulty etc, things you can do in the game, to turn a match around, or get out of a situation. This can be considered to be described as the overall game's engine.
Playability differences per character. Human Smoke and Scorpion are virtually identical upon looking at them and their moes, but Human Smoke is ranked #2 in UMK3 and Scorpion is ranked #14. The reason for this is Human Smoke's combos, and a little bit based upon his faster walking speed (ie: even if Scorp had the pop up he still wouldn't be able to perform every combo Human Smoke can)
Tier list. This is something that eventually becomes an established fact. MKII's tier list is set in stone and has been for years. The reason I point out that Reptile is the worst character in MKII is because someone said there wasn't a single bad character in MKII as a reason to like it. This is because they aren't aware of high level play. MKII's top tier consists of Mileena and Jax. Kitana has some usage as well, but not to the same level as MJ. UMK3's top 10 tier list changed significantly this year due to combo discoveries.
It is great that people still play all the 2D MK games, but when saying whether one is better than another, you can't just base it on things that a multitude of people can disagree on. There are plenty of aspects that have been described in this thread in which people can just as easily say "But I think that is better in MKD than MKII." In all honesty, the way everyone here talks about MKII, that hat should really be given to MKDA because it's superior to MKII in every conceivable way. But even still, MKDA's variety doesn't compare to UMK3's overall gameplay and tier list.
I understand it seems like an elitest concept but I have explained on countless threads why UMK3 is the best MK game ever made. It's not about graphics, sounds, fatalities, stages, storyline, character designs, etc, because anyone can have an opinion on which they like better in what game.
Gameplay mechanics cannot be argued, and you simply have to take people's word when they know more about the games that others. I myself think that MKII's atmosphere (even including the time frame in which it was released in the arcade) is a big factor. I think MKII had more intentionally violent fatalities, in most cases, people think this is better. There are however people who don't care about fatalities at all since they have nothing to do with gameplay. I understand that there are also people who don't care about gameplay at all, in which case, there leaves very little reason for them to play fighting games, except Mortal Kombat. MKII introduced blatantly "attractive" characters, like Baraka, Kung Lao, and the female Ninjas.
I think what people would have wanted with MK3 was to have the entire cast of MKII return, plus Kano and Sonya, and keep all the original fatalities, and add more. Then there is another factor, the way MK3 presents the fatalities. On top of the new fatalities being hokey in most cases, even the old fatalities were made comical. For instance, look at Reptile's "Eat" fatality. In MKII, it was a simple head eat, with a very sinister sound to it for each part, the tongue lash, the crunch, and the "mmm" all very well placed. Would fans have been satisfied if this was completely preserved in UMK3? No. They would say it's recycled garbage and complain anyway. Instead, in UMK3 Reptile's Eat fatality had multiple parts, and Reptile's head morphs to enormous size as he does it. I mean, people complain that the people's bodies don't fall down after being decapitated? Is it that important? Obviously the developers didn't think so because they clearely focused on making a good game over good fatalities.
The things that separate MKII from UMK3 in the eyes of MK fans: Fatalities, new and non returning characters. There are expandable arguments all over the internet about this, and that's all well and good since it's all opinion based.
The thing that separates MKII from UMK3 in the eyes of MK players: The gameplay. Mechanically, MKII is in no way a contender to UMK3.