Its been a while since I've looked over "Living on a Prayer"--not since I did the quest actually, but the general impression I have is that we were trying a partial summoning--not a full manifestation like the primals we fight. I think the Archons thought summoning all of the twelve at once would be far too dangerous even as desperate as we were at Carteneau. Again, I haven't looked over the quests since I did them so I could be wrong. The impression is mainly from the fact that what was manifesting at Carteneau wasn't twelve figures but twelve signs, that then started to reform Dalamund around Bahamut. We are not even sure that the twelve are actually primals, and not some remnant technology/magic or corrupted legend from and earlier era--are they connected to the Allagan? The Dalamund summoning makes that seem possible and there are some theories about this on the boards.
2.1 spoiler below:
Of course as the Good King shows us, get enough crystals and faith together and attempt a summoning and something will show up.
That's not even bringing up the rumors in 1.0 that the Archons (Thancred, Yda, Papalymo, Y'shtola, Uriangier and Louisoix) are all in fact avatars of the twelve. . . which I just did.