I just watched TLS again for the first time in ages, and I will be curious to see how they address the ending in DoFP. Although the last shot with Magneto, which I totally forgot about until I started the movie, does give an easy out for the cure.
As for some of the discrepancies, I'm not sure what can be done about the Moira McTaggarts, but I did notice that they never actually called Bill Duke's character by his full name, so you could write him off as being a different Trask, or that he was somehow related to Bolivar.
They also never actually showed Scott die or showed his body, we only saw Jean reacting to her believing that she killed him. I could see them saying that he somehow managed to get away just a second before he was disintegrated and that she forgot for some reason, or that The Phoenix wasn't aware of it.