Question: Why did Shere Khan kill Akela?
Answer: Shere Khan was angry that Akela would not turn over Mowgli to him. It was retaliation.
Question: Why was this movie a box office flop?
Answer: This was the fifth movie in the series, and it was not critically well-received. Most reviews felt it was unoriginal and unfunny compared to its predecessors and should probably have been released straight to video. With tepid reviews, audiences probably were willing to wait until it was available on DVD or streaming. Although not as financially successful as its predecessors, it did make around $408.5 million against a $105 million budget, so it did not lose money.
Question: In the tavern, the dwarves emphatically tell the huntsman that dwarven females are so repulsive that dwarf reproduction only happens accidentally, in bad lighting and under the influence of drink. Which sounds quite repulsive. But, when the huntsman and male dwarves are later captured in the net trap, the female dwarves turn out to be perfectly lovely, even quite sexy. Then, even stranger, one of the male dwarves later apologizes for the appearance of a lovely female dwarf (who is standing right next to him in plain sight), claiming that she was hit in the face with a rock. So, what was the purpose of the male dwarves obsessively lying about the beauty of female dwarves? Or were the male dwarves blind to true beauty for some reason?
Question: In the very last scene, we see Michael Shannon in shackles (presumably in a federal prison) with electroencephalographic sensors attached to his forehead and scalp, oddly gazing at the sunrise as two prison guards flank him. In the very last shot of the film, a closeup of his face, we see his eyes faintly glow for a split-second as he smiles a very slight smile. Question: Is the film implying that Alton is in otherworldly contact with his father, or that his father absorbed some of Alton's otherworldly power; or is it implying that, being the boy's biological father, he was the source of Alton's power? In any event, this may never be revealed, because the film barely made back one-third of its $18 million production budget, making the probability of a sequel highly unlikely.
Answer: I wasn't sure what to make of it, but I got the impression that he was communicating with Alton like he had done when Alton ran from the truck. I also thought his smile was perhaps in reaction to what Alton told him and/or the two were making fun of (mocking) the use of electrodes because they knew the electrodes would not have any effect on him.
P.S. Plenty of lousy movies have had sequels, so it is possible there could be a "Midnight Special 2".
Not necessarily holding my breath.
A sequel doesn't seem likely. Hope you weren't holding your breath waiting for an answer to your question.
Answer: It was a threat to Mowgli, hoping to lure him back in grief and to save the younger wolves from the same fate.