Rather than get into a long TL;DR, I thought it might be interesting to kick off a discussion and see if anyone has interesting input.
Let's start with a Wikipedia page as a reference:
https://en.wikipedia.org/wiki/Operant_conditioning
So, looking at - for example - reputation decay, we have an example of negative reinforcement. Reputation decay is a penalty for not doing something. Negative reinforcement tries to get us to do something (log in and work on reputation) by stopping decay, which is an aversive stimulus.
Positive reinforcement is a reward, negative reinforcement is a penalty. Both can be effective - in fact, it's possible that negative reinforcement may be more effective than positive - but the difference between the two is fundamentally pain vs. pleasure.
Elite: Dangerous is a game. Should you be motivated by pleasure or pain? Something to consider.
Just some thoughts, not even getting into positive and negative punishment. Reputation decay is just one example. I'm sure one could think of many others. I merely mention this since it strikes me that the above is fundamental to the enjoyment of the game, and ignoring this is possibly behind a large number of criticisms we read every day on the forums.
OK, my coffee is wearing off. That'll do.