I'd have to say the Underground Ruins. While it was fun chasing Latios around in the dreamyard, and while I enjoyed making my way to the top of Dragonspiral Tower, they didn't really come close to rivalling the regi puzzles. I may be a bit biased, since it brought a whole lot of nostalgia along with it, but just the fact that they brought back puzzles to reach the legendaries in an older gen fashion was really enought for me to be sold. And it proved as more of a challenge to actually reach the regis, than it did with any of the other legendaries in the game, which was something I also really liked about it. To be honest, I feel like most of the legendaries were pretty poorly hidden in this game, as it usually just involved triggering some kind of event, just to traverse the world, searching for whichever legendary whom you unlocked, or obtaining and item to bring out the Pokemon. And rather than including creative puzzles, they just hid them in obscure places. I mean, the Unova trio simply jumped in front of you, just to be captured by you, and it took away a whole lot of the post-game experience that's usually found in the other games.
And that's why I enjoyed the regi puzzles the most, since it was a bit more creative than the rest, and actually involved a puzzle, rather than just requiring that you step on one specific tile, that's placed somewhere that you wouldn't think of. Not saying it wasn't fun to hunt down the Pokemon, just not nearly as enjoyable as I've experienced in other games.