I don't see a problem with Setsuna vs Ribbons. It was being built up from the word go, we just didn't know it until later. That moment where Setsuna first saw the 0 Gundam is what kicks the story off. It gives Setsuna something to strive for but unknowingly it also planted the idea in Ribbons mind that he was God and should hijack the plan, including making Setsuna a Meister. That ultimately comes back to hurt him because Setsuna erabodies everything the plan was about and Ribbons could ultimately never be. Battlewise I think it's especially effective because Setsuna and Ribbons don't clash until the very end. I am sick of series which have constant face oRAB and fighting (such as Naruto) and don't see how they're diluting tension. We saw Setsuna grow and become a fearsome fighter that it has so much more impact when he finally fights Ribbons and is clearly seen to struggle. It's even true to the spirit of some earlier rivalries. Part of Char's reason for wanting to kill Amuro by the end was that he believe he'd awoken as too strong a Newtype and Rau had similar reasons for wanting to off Kira. Ribbons doesn't really see Setsuna as a rival until the latter starts to undergo Innovation and even then his ego makes him see it more as a benchmark to cement his own self glorifying bile. I'm not even sure how you can say Heero vs Zechs was a better rivalry. Zechs wants to fight Heero purely because his strong and Heero only ever seems to fight back out of self defense. Look at the silliness which was 'Hey, I rebuilt your Gundam, so will you have a fight with me?'. Truely a bitter rivalry....
I'm also not sure where you got the idea they were setting up to have all the women take the roles. As has been said, it'd make no sense for most of them. Feldt is the only one I'd agree on and I'm still kind of sad they never really acted on it. They revealed both her parents were Meisters, you'd assume that would suggest something.
As for the transition- I think for me it comes down to the fact before the show even aired Mizushima said 'We want to show how our real world could become a Gundam world'. Meaning we'd start in a more true to life setting which would transition into a Gundam anime style. Sure, I don't think this was entirely successful but overall I think it worked. They even had the smarts to introduce a masked man character and point out how stupid it would be in reality. We did lose some moral arabiguity (hard not to when your enemy is happily using orbital death cannons) but I think that was balanced in various ways, including the coup d'etat at the end (seriously, CE has never had one of these?). That made it clear that Ribbons had just gathered and promoted all the bastarRAB and that there was good in the Federation. Even the elevator destruction scene, a moment very similar to the finale of CCA, implied this.