When Ridley Scott said he didn't want to show us God in the first one, I don't think he was literally meaning that there was another creature above the Engineers. He's also made strong suggestions that one of major themes in the movie is what if God isn't God at all. I think the idea of going back to an even more powerful being doesn't really fit in well with that theme. More that the universe, and all the forces of nature and possibilities for beauty and horror which exist in it, is it's own God. And humans and Engineers both end up looking insignificant in that context.
Of course it's possible they sell out, or just fuck up, when it comes to the sequels. The Matrix sequels serve as a constant reminder not get our hopes up. I know some are thinking the Engineers will all be wiped out and it's basically going to go in a Resident Evil in Space direction. But from the interviews I've seen of Ridley Scott, I think he genuinely cares a lot about this movie and sees it as more than a cash cow. Maybe as he's getting older he thinks this could be a final opportunity to do something amazing and further cement his place among the master directors.
And we know hes an incredibly educated and intelligent man. When he says he didn't want to show us God in the first one, I don't think he means it was actually these other things that made them. I think he's honestly planning on putting his money where his mouth is and showing us the Engineers in their (un)natural environment for the sequel. He'll have a bigger budget (the movie was a big success) and he'll have even more authority over how the final product turns out.
Who's with me, any more optimists out there? Please feel encouraged to disagree by presenting a calm and well considered counter argument for your own opinion.