Joker, your helmsman and the "best pilot in the Alliance," is either a bad pilot or a horrible human being.
When you land on an alien world - that is, when your pilot drops you off and flies away to laugh at you from orbit - look around for the largest, roughest, most difficult mountain. Invariably, your destination will be on the opposite side of that tortured geography. The game makes a big deal about the fact that he suffers from brittle bone disease, but that doesn't explain why you spend the non-elevator portions of the game bouncing around on jagged alien topography when you have a spaceship at your disposal. His biggest problem isn't his bone density, it's that he's a jerk and he hates you.
Shamus Young is a programmer and writer by trade, videogame nitpicker by inclination. If you have the patience for more of his ramblings, they can be found at ShamusYoung.com.