Teal Mask gets points for its story. That's how legendaries should be done, with an interesting plot and lore execution. Compare with Terapagos, which is basically just thrown there at the end without any build up... it can't even hold a candle to Ogerpon and "the loyal three" arc.
Indigo Disk gets points for the battles though. Some really good and challenging battles if you kept caps under control and aren't cheesing through it with a level 100 team. And I also found Blueberry more interesting than the Kitakami region.
So, I prefer Indigo Disk because it's better at things that matter more to me. Teal Mask has a good story for Pokémon standards, but that's not saying much because Gamefreak is just bad at storytelling.