One thing I would like to see is for spiritual matters to be available to everyone. More specifically, I hope that spells of the shugenja are not the primary way of handling such matters but rather that spells be an outgrowth of whatever system is created for dealing with spiritual matters.
With regard to the scale of Rokugan, while specification of exact distances and population sizes may lead to absurdity, I feel that it may be helpful to give guides to travel times between major cities and rough estimates of population of those cities. Another thing that could be helpful is if a clear relationship between population and area of regions were devised, as that could help authors avoid absurdity.