Baby Luigi said:
1. How did Tabuu steal the Halberd? It simply appeared after Mario and Kirby battled each other.
His hench-men stole it while Meta Knight wasn't looking.
2. Why did Tabuu try to control the world? Where is his motivation?
For the plethora of reasons why anybody wants to rule the world.
3. Why did Rayquaza attack Fox and Diddy?
Why did it attack Deoxys?
4. Why were Mario and Luigi separate? They are usually seen together when they are adventuring yet they are in very distant lands. Their relationship is never shown in the whole story.
Relationship is already known. It's not impossible for them to become separated, it's just the likelihood of happening isn't really great.
5. Some of the unlockable characters' places are in really bizarre locations. An example of the Pleiades and the Lylat Cruise stage appearing in The Cave
Never gave too much thought on it.
6. Why did Kirby have a shorter duration to recover when a Dedede badge is attached to him?
It's basically an inanimate object trying to give an animate touch. Plus they could of been timed.
7. How did Bowser, Ganondorf, Wario, and King Dedede even begin working in the dark side?
Because they're evil and greedy and all want to rule over a vast dominion.
8. Where did Sonic come from? He just appears spontaneously.
That's Sonic
9. In the scene with the giant canon, where did the good guys obtain their vehicles from?
We don't really know how much time was given between those two scenes, so they could of got the vehicles from where they land it or they were already in one of the ships.
10. In one scene, Pit can fly, but in another, Pit suddenly can't.
Correction, he was gliding, not flying. It even mentions somewhere in the game that his wings are too small for flight.
11. According to the Shadow Bug trophy, Mr. Game & Watch is filled with the dark stuff. Why him?
Because he's a rather mysterious character. It's like saying why are plants green? Because the chlorophyll in them is green, maybe the same logic here.
12. Why did Kirby suddenly abandon the princess in one scene?
To me it seems more like either a "stay here, I'll be back" or "Somethings over there, I'll investigate."