I've got a few pets dedicated solely to missions, I take it I attune them to an element and just raise the state they're dedicated to...any suggestion on which element for which stat raise?

For proficiency points, I don't think the element affects it much. The stat gain for each point should be the same no matter the element.

The only thing would be strength or intelligence. You can't increase intelligence on a strength-based element, and vice versa. You'd have to use a earth, air, or water for strength, and shadow, light, or fire for intelligence.

This guide does a good job of explaining that kind of stuff: https://www.sylestia.com/forums/?thread=12841