The most common gripe I hear is the ship controls. It's really designed for controller, and manual space flight is kind of pointless when the autopilot can do it so much better (as long as there's nothing in the way).

It's really a game about pulling threads until you find interesting things. The ship's computer is useful for keeping track of the thread ends. Most places can be reached in a minute or so right from the main planet, although depending on where you're going you might have to wait longer to get access to what you want. There isn't really any "starting over" because what you're gathering is knowledge in your own head.

I think the hardest part initially is finding an interesting thread to pull on. I think Giant's Deep was where it started to click for me, but there's undoubtedly more.