The short answer is that this is an open source project with code form multiple authors, so there's certainly room for improvement and optimization. The out-of-the box import is intended to just be simple jump start for the inevitable customization. I hope the community will take advantage of GitHub to file issues and submit pull requests with code changes & additions.
Longer answers:
Shashidhar Gurumurthy wrote the scheduled import and associated settings, so I'll let him explain his design.
The Site Metric object is fairly flexible; a nice addition would be to populate the Metric field picklist with all the valid values for Google-definied metrics. I'd be hesitant to store something along the lines of a Google Query Explorer entry, since the complex filters and other fields would be difficult to validate. For incremental imports, the dates would also be in flux.
Salesforce does support complex unique keys based on multiple fields, though it requires some effort. It would also be complicated by the fact that for any given metric and date, you might have multiple records for different filters or segments. The approach I've taken on projects where we update existing metrics is to query for existing data, add any new records, and then upsert the resulting list.
Matthew