I would say that if you want to be analytical, at this point in the discussion physics and cosmology have to be analyzed together with theology.
There's the question of what is the arrow of time? Does a universal time exist outside of areas of linked causality circumscribed by light cones (limited, of course, by the speed of light)?
By the definition of omnipotent above, something that exists throughout at least a large part of the universe travel is being described - ie. both inside and outside of our local light cone. Therefore it would likely exist through FTL effects (like quantum entanglement) or travel around at FTL speeds, and essentially exists in what we call the "future," the "present," and the "past."
That then raises all the typical time travel questions. Does changing the past cause the universe to branch into two new universes? Or does it change the timeline of the one existing universe? Or is there a temporal protection mechanism that prevents the "past" from being changed? Does the temporal protection mechanism mean that all influences from the "future" were already included in the past all along?
There's a saying that's been around for a while now: causality, general relativity, FTL - pick two out of three. All three can't be true. And general relativity seems pretty well proven.
So, if causality is immutable and there is a temporal protection mechanism,
and a super-intelligence which exists outside of one limited light cone, then that entity would have highly constrained if non-existent free will.
If, on the other hand, the universe is less causal than we imagine (which I suspect is a strong possibility), an omnipotent or near-omnipotent entity may have the capacity to change history in order to cause the universe to take on forms that it prefers.
So, a God might exist outside of local time and yet also have free will. We really don't know enough about the universe to say one way or the other. Until we come up with a grand unification theory of physics that has no glaring holes in it, I don't think we can say. At this point I see no reason to trash people's belief systems, given the limited information available. I only see a reason to say that people should keep their beliefs separate from science. This doesn't mean that they should keep morality separate from science - I think any reasonable person can see that, say, the scenario in "The Island" is wrong - you don't create thinking clones and then murder them for spare parts. But you also don't postulate intelligent design when there's no evidence for it.
I am willing to agree that we're not sure how life first started, and it's perhaps slightly possible that something intelligent created the first cells on Earth, or else created them on some other planet and then spread them here through an act of panspermia. Or perhaps it didn't even do that. Maybe it just made the universe have the various physical constants that it has, knowing that with those specific conditions planets would form that would have the necessary conditions for life to arise. Maybe it's one of the laws of this universe that life arises where the conditions are right, just like stars form out of gas clouds. No way to really know about that either until we get a sample larger than one. I would say we can't really say until we've studied several thousands planets in "goldilocks zones." Even if life only emerges once in every several thousand star systems, that would mean tens of thousands of planets with life in this galaxy alone.
What I can say is that once life as we know it came into existence on Earth, it has evolved through natural selection. Humans evolved from prokaryotes through eukaryotes through chordota, fish, amphibians, early reptile-forms, therapsids, early mammals, primates, early hominids. Various suboptimal structures in the human body indicate that the morphological changes arose through mutations that were beneficial and then selected for, but not the best possible design. Something doing precise intelligent intervention would, say, have designed our knee joints better. We got "good enough" through natural selection.
So what I am trying to demonstrate here is that a rational person can believe in God and also in the scientific method, and such things as evolution through natural selection. Heck, IIRC even the Vatican's position these days is that evolution through natural selection is correct.
Personally, I'm an agnostic: as you might guess from what I wrote above, I think we have far too little information to currently judge what's going on in most of the universe. I see no conclusive evidence of God, but neither any conclusive evidence that something you could describe as God does not exist. From my perspective, to be an atheist and be certain of the non-existence of God requires a great deal of faith, just like religion does.
And, for the sake of tradition, I'll respond to GIThruster's Merry Christmas: Merry Christmas too to everyone here who participates in it, whether as a religious or simply a secular-commercial event!

And Happy Hannukah, Festivus, Quanza or whatever you celebrate to any other reasonable people on here!