WHM has generally seen enough improvement that the majority of their traits, abilities, and spell at least serve some purpose. (yes, even stoneskin)
All the Cures and Medica have obvious application, but because SE renamed their spells, the Cure spells are a bit confusing at first glance. With Cure I and II both being single target, you're thrown a curve ball with III, as it's an AoE like Medica... but not like Medica. Unlike Medica you can cast it from afar and basically "bomb" a small area with a Cure less effective than your Cure II. It serves some purpose obviously, but generally your Medica spells will serve you better as Cure III seems to be intended more as an emergency device. If you actually manage to trigger Overcure, and you also just so happen to be in a situation where you think to yourself, "Wow, I could use an AoE Cure right about now!" then Cure III would service you much better.
Obviously, the situations which call for Cure III will be less apparent than those that call for Medica, but it's there if you ever feel you need to do some faraway Cure bombs.
Holy is actually pretty nice for FATEs with large amounts of monsters and people, plus it's satisfying to set off a Holy Explosion and actually contribute in some pretty fair damage for once.
Shroud of Saints is your ONLY ability that helps you retain your MP. It would be wise to use it often during fights that may tax your MP reserves regardless of your Enmity situation.
Presence of Mind suffers from a stupidly long cool down, and you might see little benefit in the 10 seconds it gives you at first, but if you pair it with Divine Seal, you'll be dishing out HP like nobodies business.
They generally share the same sort of abilities, and while SCH has obvious advantages, they also can't cure as well in a tight situation like WHM can. When your party gets hit by an AoE and all of them are standing on their last leg, WHM can recover from this situation much more quickly than a SCH could.
Also, despite SCH originally being advertised as a HoT job, it is not. They only posses one HoT and only the Fairy Eos has access to it. While she casts it frequently, it is not always available and she is difficult to micromanage on your own to have it cast on demand.
WHM's Regen is far more accessible and powerful.