It has a lot of depth within its narrow confines - it does what it does very well, and its mechanics are certainly more complex than they initially seem.
But I wish that the depth went beyond just customization, stat boosts, etc. There are a metric ton of spells, but many of them are very similar to each other. I also don't really feel that the elemental system is creative or fun - instead of making me change my gear set to best fight enemies based on their unique fighting styles, I choose based on the arbitrary elemental weakness the developers have saddled them with.
This design choice is probably a consequence of the fact that the bosses are, like the spells, too same-y. In Dark Souls (a tired comparison, I know), each boss forced me to play the game a totally different way. There wasn't some "weak spot" telegraphed to me - I had to discover their vulnerabilities for myself and alter my approach as needed.
And the "branching missions" as you call them are probably not the best example of depth to use...