I'm kind of torn between the two eras. I know the series' return to its dark roots in MK4 and Deadly Alliance was widely popular but I've always liked the cartoonish, over-the-top stuff they were doing circa Mortal Kombat 3, with Friendships and Babalities providing some comic relief. That generation of the MK franchise was a lot of fun back in the day.
However, I do really like what they've done with the series in recent years, expanding the storyline further, giving characters deeper backgrounds and making the MK universe much bigger. To that end, Deception is one of my favourites because of its long Konquest mode that has a timeline that's somewhat flawed but weaves some of the established storylines together. They've come a long way since the story was basically seven fighters trying to defeat a four armed monster and an evil sorcerer who were running rampant over an ancient tournament to determine the fate of all existence.
Armageddon was a fine game too but the lack of bios has bothered me since the game's release since it left a lot of holes in the ongoing MK saga. It was cool to have such a huge roster of kombatants but since many of them were killed or otherwise unaccounted for in previous instalments their presence in the tournament went unexplained, except for the fact that they were all part of a huge group of kombatants whose battles were on the verge of bringing about the apocalypse. Also, the Kreate-a-Fatality feature was alright but I would have preferred the traditional character-specific fatalities, since that's always been such a big part of the game.
I think I'll have to cast my vote for the MK3/Ultimate MK3/MK Trilogy instalment though. It also wins points for the supreme fatality demonstration available after beating the game on the hardest level.
damn those metal arms rocked! Sub Zero is also awesome, this makes me so eager to go dig these games out now. 
