it really is kinda depressing at the start, agreed. the whole point is to resurrect the world from nothing, so it's obviously empty and barren at the beginning. so the satisfaction is in making stuff lively again, and the game doesn't really pick up much until you resurrect some more stuff.
did you enjoy, say, Okami? the premise is kinda similiar, though it has its gorgeous visuals to grasp your attention. Terranigma looks like an rpgmaker game nowadays, so you kinda have to give it a chance to appreciate.
maybe try to do the towers, and see how it goes for you from there.