This illustrates how far away we are from the Star Trek vision. The biggest hurdle is not malfunctioning sensors or other components really.
We need a totally different propulsion system. If we had "limitless" amounts of "fuel" the need for these neck breaking accelerations wouldn't exist anymore. We could climb slowly through the atmosphere and accelerate no harder than a jet plane taking off, for example. Equally, the re-entry into the atmosphere could be as gentle as we want it, no need for heat shields.
The key to future space travel is indeed a different propulsion system.
Who will invent the anti gravity generator? That would be a very nice gadget.