Crystal Bearers does.
Mechanics and puzzles can be introduced to the story to make things more complicated. For example to prevent a monster from using a move that will destroy you; you could use an incapacitation ability to break off the necessary monster part.
Want to break the protections of a monster? Pay attention to the clues in the story and make sure the obelisks are facing the correct orientations.
Want some strategy? Make the companions commandable via a pet interface and make sure their AI isn't ragged. Now your companion healer can cure and you can control it [or even multiple companions]. You can tank in a position that is most suitable, or you can send your companion into a kiting scenario.
This isn't an insurmountable issue. Challenge is not the essence of a group.
