The only ways to increase the damage of these X-X damage skills are by increasing your bonus to magical damage.
You can do that either with specific items, or by increasing your focus.
Note that critical damage also applies to these skills, if they are not DoT (Damage over Time).
Actually, if you have a character with a lot of +% to crit damage and crit chance, combined with a high focus, you can reach absurd high levels.
But yeah, if you want to go that way, then the weapon dps is useless, and you will want to prefer weapons who increase your casting rate for example.