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Explorers of Sky.
Storyline of second PMDs was better, I love the minigames, Spinda Cafe, SHAYMIN, Giratina Origin Forme and mainly RIOLU as a Starter.
Darkness would be the best in my decision, because I haven't played sky yet, but I will once I finish darkness and then find out how to get sky, since romulation won't let me download it >.<
I haven't played the third but what I can judge is the other two game titles I've played. And so my answer would be PMD2. Because I thought everthing was updated better story wise was a little bit better.
Well at the moment I have Red, Blue, and Sky. Even though I've only been playing Sky for a couple days I already enjoy it a lot more than the originals.
I like Explorers of Sky more because it has a better story line and better pokemon to choose from whether it be the hero or the partner.