I find it odd, though welcome, that there never was a truly direct conflict between the Founders and the Prophets during the Dominion War arc. Of course, the Prophets disappeared the Dominion fleet in SOA, and Weyoun makes some comments about which group truly deserves to be worshiped. Even that act of interference only involved an aspect of the Dominion, and not the founders directly, and almost entirely with respect to Bajor. (Not to mention, Sisko had to dare them to take action.)
The Founder and the Prophets were the most deeply explored godlike entities in Star Trek. However, their interests would have been asymptotic had it not been for Sisko being both Emissary and architect of the Federation war against the Dominion. It would have been easy to slide into a more direct conflict between the two, the fluidity of the Great Link vs incorporeality, compelled devotion vs inspired revelation, the way that each related to the future. I think all the comparisons betwee the Founders and Prophets would be interesting, but I think it was for the better that there was no war between the deities that paralleled the larger war.
The Founder and the Prophets were the most deeply explored godlike entities in Star Trek. However, their interests would have been asymptotic had it not been for Sisko being both Emissary and architect of the Federation war against the Dominion. It would have been easy to slide into a more direct conflict between the two, the fluidity of the Great Link vs incorporeality, compelled devotion vs inspired revelation, the way that each related to the future. I think all the comparisons betwee the Founders and Prophets would be interesting, but I think it was for the better that there was no war between the deities that paralleled the larger war.