I would suggest doing any levels that have risky skips/glitches in them first and the easy/consistent levels toward the end. Keeping that in mind, you should also try to keep the transitions between levels as short as you can. I don't run the DS version of this game so I can't really give you a specific level order, just general tips.
I'm sorry I missed this - The best way would be to start with either Chapter 1 or 3, in level 5, to save time on movement between levels. In the final chapter, which would be either 1 or 3 depending on which one you did first, start at level 1 to save movement. This is the case for Hero or Villain runs. However, for All Levels runs, it would be best to start at either the end of Chapter 1 in Hero or the end of Chapter 3 in Villain. Although I believe when leaving the asylum you're sent to the center of the Batcave so that would mean it's best to start in Hero C1.