Yes, they first introduced that in DS9 I think, but it was near the end and not fully developed. I felt like the Dominion war, while still pretty well written, took the microcosm that made DS9 special and tried to turn it into War and Peace. There were so many ideas that some of them faltered. DS9 explored the ideas of shifting alliances and ulterior motives, but at the same time gave it's "villains" more sympathatic betrayals than in any previous iteration. I mean Gul Dukat was one of the most well rounded adversies ST has ever produced and you got the impression that Sisko really respected him even if he didn't trust him.The Founders were interesting, but more of a return to the outsider threat. I think section 31 could have been worked into the Cardassia/Bajor/Maquis dynamic just fine and would have had given it more room to grow.