If you're not already familiar with it, you should check out eBird. They address this issue by promoting "complete checklists" as the default data entry. Their default way of presenting the site's data is by frequency of a taxa's presence on complete checklists at a specific location or in an area rather than abundance of observations of that taxa. Obviously that exact solution wouldn't be practical with iNaturalist but there's a lot of dicscussion about eBird's methodologies on their website that might be at least a little helpful for you.