Okay, tell me what you think:

Cthulhu and his old ones vs. Dagon and deep ones.

Could you tell us a little more about your concept? Are you thinking more along the lines of an apocalyptic battle between the two, with mankind caught in the middle? Or did this conflict happen in elder times? (If so, it could fit nicely with the war Lovecraft describes between the star-spawn of Cthulhu and the Elder Things.) Or are you going for a more Godzilla-like feeling, with giant Mythos beings battling each other in modern-day cities? Is the conflict the background for the story, or is it the story itself?

Ugh... Well, Its in modern times, yes. Maybe with mankind cought in the middle. I'll work that out. a Godzilla like feeling would be nice (I'm a HUGE Godzilla fan) and yes, the conflict would be the story itself.

Well in accordance to Lovecraft's stories the Old Ones did have the power to control the deep ones. Though such and engagement would be a great battle, I believe the eventual outcome would be the Old Ones being victorious.

Right, but remember that the Shoggoths were controlled by the Elder Things, yet they were able to rise up against their masters. Something along those lines could be very interesting... The Deep Ones grow tired of serving the Old Ones, and their lord, Dagon, leads them in an uprising. I might be projecting human motivations onto something totally alien, though.

Sole Man, this is your idea. What are your thoughts?

Yes! That's exactly what I had in mind! I think that would be cool, don't you? An epic war between the two greaest creatures in the unvisrers... What do you think?