I've very much enjoyed the Dresden series as well. I have a few suggestions some of which are based on Marcone.
Countering the PC's: Don't set it up to directly counter the PC's. Consider it from the viewpoint of the boss villain. Make a plan to counter the most common abilities of adventurers, not necessarily the PC's personally. At least some of the countermeasures in place should be obvious or poorly kept secrets, which will let the PC's plan and get the upperhand. Let the villains adapt, but make it clear that they are not the only threats out there.
Recurring villain should not be the main villain: Recurring villains work best as a thorn in the side, rather than the penultimate worldender. You can up the ante by occasionally forcing the PC's to work with/for the recurring villain.
Escape Clauses: a:) The villain has standing and cannot be directly attacked. Guild head, noble, crime lord. b) villain is somehow protecting PC's or others from a worse alternative or c) Not in their best interest to deal with permanently. They could be a henchman who flees once things go south (and the PC's don't have time to chase him), or is simply willing to sell out.