Why is Alice so protective of Becky? Because there's about 1/25 chance (assuming half the base clone types are males) that she is actually her own clone!
Which explains why her face comes close to showing horror when they meet. She just sighted the Moral Event Horizon.
What exactly does the "Retribution" in the title stand for? It's referring to Jill, who, after being overshadowed by Alice and not getting to do anything cool in the series, finally gets to beat Alice to a pulp this time around.
Why does the Japanese woman from the opening of the previous film appear as a clone model in this one? Umbrella started the outbreak deliberately by releasing that infected clone inside of Tokyo.
Ok, Wesker is now the "good" guy. So, the Big Good is a superhuman nigh-unkillable egomaniac who eats people. Though he could be using his game counterpart's serum now instead of a high-protein diet...
As the final film showed, Wesker was never a good guy in the first place.
If Alice and Jill had lost the final fight, Becky would have been left behind, as she was still hidden in the snowmobile-jeep-thingy. Or worse - she would have been eaten alive when the zombies broke through a weak-spot in the ice.
