I think however the best for it right now might be Chris Columbus if the whole look and feel of the first Harry Potter movie was anything to go by. Especially for Lovecraft's "Dunsanian" fantasies like Ex Oblivione or Hypnos. Although the noir vibe Zack Snyder does so well (Watchmen etc.) could work too with Lovecraft's darker mythos tales such as The Shadow over Innsmouth, The Shadow Out of Time, or At the Mountains of Madness.-40hz
Columbus would be an interesting choice. Before the Harry Potter movies I dismissed him as a second rate hack. In retrospect he was just stuck with a bunch of third rate movies. The first Harry Potter movie completely surprised me for just that reason. Chamber of Secrets made me a believer.
I'd still take Del Toro though. I think the biggest challenge to putting Lovecraft on the screen (big or small) is sustaining the creepy feel and IMO he's the master. The Devil's Backbone and Pan's Labyrinth are both full of that.
I hadn't thought about it much until I read Stephen King's book, On Writing, but the other big challenge is the lack of dialog. King was actually mentioning it as a positive by pointing out Lovecraft didn't like people so he was wise to avoid it. Even if you could pull that off - and it's not impossible - I can't see a studio allowing it.