Processing done in Map/Reduce scripts should be work that is not dependent upon order and where each unit of work is isolated from the others. If there are any kinds of interdependencies, then a Scheduled Script will be needed to properly order the work and retain any aggregate values.
However, while you can’t control the order of the values received in the reduce phase, you can always simply sort the values array using a custom sort function, so that is one area you can have some control, if needed.