I'm sure it will pick up eventually. Ys games always had a fascinating story to me. Of course it shares its similarities to the Zelda games with the exploration and treasures.

As for your allies in the game? Is there a way to change their tactics in the inventory screen to change what they do? Memories of Celceta is the 2nd game in the Ys franchise to use a party system. Before then it was a 1 person adventure.