Hey that's your opinion, I imagine not a particularly popular one on this thread xD
Like everyone seems to be mentioning, the more fleshed out character personalities were a big one. I mean, even Bianca's dad gets a scene with some emotional music :P
But seriously, Alder and N are great characters. N particularly went well for me as I'm really into Assassin's Creed, where most of the Templar Order also believe they're doing the right thing despite their methods (and likewise, the Assassin's kill loads of people because they believe they're right too). The mixing-up of his team, and more frequent battles, was really cool too. I hated how you only got one battle each with Archie and Maxie, and Cyrus in DP. It also served to highlight some of the pokémon you may have msised in an area if the high encounter rate started to get to you.
The whole thing with the Pokémon League in particular was very well done, highlights of it for me were; Reshiram / Zekrom appearing to not believe in you - and the idea that you might have to fight N with just your normal team, Reshiram and Zekrom's signature moves being powered up with cooler animations against eachother, and Ghetsis' reveal (he had really atmospheric battle music too).
The latter point in particular - there are loads of little verbal slips from him throughout the story, but by this point you get so caught up you've forgotten about them so the twist still works.