I think there are lasting consequences of the events of 2.55 but they just don't include deaths. To be honest, I didn't think any of the Scions were dead at the end of 2.55. I thought Nanamo was the only dead one. Sure they could kill of Minfilia but it would be a pretty lame way of ending the character, particularly since all the other scions we see facing deadly situations and Minfilia just runs off into the sewers on her own.
Personally Nanamo is the death I think was wasted. While I like the character, by far her death had the biggest implications and the greatest impact storywise. That would have shaken both Ul'dah and the Alliance to the core and forced several Ul'dah characters and institutions to evolve and step up. It would have also forced real development with Ul'dah's own story which has been tied up with the Monetarists since 2.0.
Simply put, after all the rest, Minfilia's death off screen would be pointless impact wise and wasteful character story wise.
Minfilia is unpopular for plenty of reasons which are perfectly justified. I just cant help myself correcting people when I see them stretching the facts on the character to justify dislike of her when it simply can be summed up by the fact she doesn't do much we actively see and she, like the rest of the scions, hasn't been developed much. The other scions get some forgiveness because we see them being active in the field. The thing with a manager is generally you only notice the results when things go wrong so their contribution can often be undervalued and from a narrative perspective its hard to clearly define value to the role for the action based player.