Egil sacrificing himself to save Shulk was to help screw over Zanza, as he was only trying to kill him through the deaths of others. Shulk never really wanted to hurt Egil, and would have gladly helped him if he had agreed to stop assaulting Bionis. Fiora coming back had a good plot reason, because Meyneth wanted to be close to Zanza and the Monado and try to deflect it's influence. Fiora was the perfect vessel for the job. She was also extremely capable as a fighter, and many less important Homs were turned into faces, so her being used wasn't that strange. Lorithia was always part of Zanza's group, and was in on it with Alvis, as is seen in a few scenes around Prison Island. It was always Mechonis Vs. Bionis, because it was Zanza vs. Meyneth. Zanza attacked Mechonis through Bionis. So the Machina would obviously oppose him. The people of Bionis were fighting to prevent their extinction. Zanza would have given it to them. Earlier in the game, their are hints of Shulk achieving the true Monado, one that is his own. That can give him the power to survive an ether shot. Some of what I said is from cutscenes that you just saw, so I think that you weren't paying a lot of attention. You shut yourself off and then posted a problem that was resolved by the game. Most of what you had to say was oppinion based/not easily remembered, so I think that you still have a point to make, but the first half of the game was a revenge plot. Fiora died. Go out to kill the thing that killed her. Other people had loved ones die. They join your quest. That is cookie cutter plot.
P.S. Fiora was mostly being kept alive by Meyenth's power, and she had limited time once Meyneth was gone.