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I haven't read past the first volume of DP, so I'll say the Hoenn Saga (Ruby/Sapphire).
The Manga added a story where the games didn't have much of one (Yellow's was totally original and would've made a great plot for a game, I think). But the RS games (and Emerald's extra bits were added later into the plot) already had a story and the manga evolved it into something better. I like how Gym Leaders and other NPCs in this comic get more involved than anywhere else.
DP is a very boring take on the series to me. We have one rich girl and her two "bodyguards" (comedians who wound up with the role after accidental mail swapping). Gyms're only a side-quest. Haven't seen Galactic's involvement, but I read that it's much closer to the game's (Valley Windworks), while Magma/Aqua did a few other things on top of that (abandoned ship).
And I just don't like Dia and Pearl's jokes.
Everything in the manga always serves a bigger purpose than what it initially may seem like...Defeating the Gym Leaders is much more than a side-quest as you'll see much later in DP. Same for the Platinum saga; Platinum defeating the Frontier Brains serves a much bigger purpose than it seems.