Personal preferences and all, but I find that other than Atelier Iris 2, none of the Atelier games has a story that's supposed to "pick up." True there is always a main plot that goes straight through the entire game, but most of the time the attraction comes from the various (often unrelated to main story) scenes and side-stories instead. And I find MK2 to be the most enjoyable in this aspect, the jokes are funny, and just seeing how the NPCs' dialogues change after each chapter is enough of interest for me.
Also, I'm the type of player who likes to explore everything in a RPG, and the traditional style Atelier games with their highly strict time-limited system don't allow me to do that. Meanwhile with the more RPG-oriented games (Iris and MK series) I can do whatever I want at my own pace without worrying of running out of time and getting a bad end before I could even set foot into the later dungeons.
Then there's the battle system. To be honest I find the Arland subseries' battle system to be quite slow after what Mana Khemia and Ar tonelico delivered. MK2's battles are so upbeat and involving that, by endgame, the speed is almost comparable to a real-time battle system, yet at the same time is still turn-based. Characters flying switching in and out, doing multiple hits in a flash, etc. And there are also the battle themes.
In fact, the only thing I don't like about MK2 is its opening movie, half of which features still images instead of the usual anime animations, the other half is wasted on a wriggling fire-breathing big fat dragon that doesn't even appear as an enemy in-game.
But eh, it's all opinions.