That one is tricky also. For example, some people have around 20+ sockets in their gear. Some barely have few. It's no one's fault, both items are nice (with or without sockets). It might be a good idea to measure the overall quality of gems tho, not the amount of gems, and give small bonuses according to that. It's definitely worth to think about.
As well as a weight scale, This gives you 4 points to play with for weighted items. It also rewards those who invest into their gear. However some items can gain +3 item level< but with epic gems it does make the gear a bit better, thus increasing it's comparative level.
On a side note: The site looks fantastic, keep up the great work!