I'd love to see environmental effects modeled. Not too realistically, of course, but if you go to, Moho, for example, you need to bring along proper cooling equipment. Heat management would actually be a nice challenge for long range manned spacecraft to Jool or Eeloo, for example, both to prevent overheating, and to maintain enough heat to keep the crew alive, or keep scientific equipment operating for probes. Or, you'd need pressure suits and robust equipment for the surface of Eve, due to the thick crushing atmosphere. Radiation would be nice, as would space weather like solar flares. So basically, environmental hazards. Aside from that, resources for mining would be nice, as would a pre-flight planner allowing you to plan all burns before you launch. A display in the hanger showing you the weight, fuel, and delta V of both the entire spacecraft and on a per stage basis would be nice as well. And, as others have said, an asteroid belt with a dwarf planet or two would be awesome, as would comets. Maybe even let us make space "tugs" to allow us to recover asteroids for mining, or move one out of the path of a space craft. Dynamic environments would be another awesome addition, allowing us to make impactor probes ala the Deep Impact probe. But mainly so I can see all the craters around KSP Control from the failed launches.
