Just to be clear, I'm in the "almost never use it, and don't use it to fix design flaws" camp as well. On the other hand, I'll use it in trivial circumstances when it doesn't make any gameplay difference, and doing it the right way would be more trouble than it's worth. For example, I recently did a retool of a FAC shipyard to a new FAC design (don't remember the difference). About a week after the retool finished (after I had launched a build but before any were completed) I researched small engineering. It wasn't worth it to me designing a new class, retooling the SY yet again, then refitting the ships under constuction up to the new standard just to trade some engineering space for a little fuel, so I simply changed the design. Prior to that, I can't remember the last time I changed a design. A few (game) weeks later, a similar situation showed up when I researched 50% thermal engines. In that case, I went ahead and did it the "right" way, since I considered the difference in engines significant.
Since most of Aurora is single-player, I put this in the same category as cheating at solitaire - I trust myself enough not to cheat to not want Steve to limit my ability to modify reality in a non-cheating way.
John