Switch over to the Shipping Zones functionality
WC 2.5 added shipping zones, which allow multiple instances of the same plugin, and also already provides geographical restrictions.
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Read up on Shipping Zones -
Implement shipping zones in general -
enable instance-based settings -
Figure out a way to migrate global settings to zone-based settings -
Or find a way to provide a legacy method class that uses the old, global settings if the plugin was used in the past (see class-wc-shipping.php, function get_shipping_method_class_names) -
Add rule syntax help in the method's config pages -
Add upgrade nag box in method's config pages -
Update documentation on the homepage -
Update screenshots at http://wordpress.org/plugins/