Having Bob and Julia team up, despite them not having any relation whatsoever in Tekken canon is part of an elaborate Shout-Out to Full House. You see, Julia's mother is named Michelle as in Michelle Tanner. Then we have Bob as in Bob Saget who played Danny Tanner.
Why is Bad Box Art Mega Man so out of shape? He's been sat on his couch for the past 20 years plus, eating chips & waiting for Capcom to pick up the phone. Which also explains why he's so excited - "This is [his] destiny" after all.
Alot of people noted the similarities of Ogre resembling Seth of Street Fighter IV fame. The brilliance comes in upon noting that Ogre's playstle in Tekken 3 was him using moves from other characters, the same applies to Seth.
Why is Heihachi Mishima the only character who does not succumb to Pandora? Aside from being made of pure badass, the Tekken 4 storyline had hinted that he could actually be immune to such things (though, in that game's case, it was referring to Ogre's DNA and Tekken 5 cemented that he is the only Mishima who was completely unaffected by the Devil Gene.) The intro of Tekken 6 can also lend credence to the theory that even if that wasn't the case, he can resist it purely out of sheer will (such as when he recovered after being blown to kingdom come and smashed into a grave.)
Ironic that Nina is with Kazuya right? Her ending with Kazuya makes more sense if she's Only in It for the Money. Someone (likely Jin, if her Tekken 6 plot is to be followed) probably paid her more than Kazuya is dishing out.
In both this game and Street Fighter IV, Ryu gets a few titles, as well as a few lines, about his liking of beans. At first, it just seems silly, but then you look at win quotes from Alisa and Asuka toward Akuma about beans warding off demons, and then you remember that Ryu struggles with Akuma and the Satsui no Hado...
Why is Abel suddenly more childishand kooky than in SFIV, aside of invoking Rule of Funny since his partner is Guile? Well, not only Abel himself is barely out of adolescence (Word of God says he's 16-17 tops), but his whole life has been spent either in labs (whether as a Seth clone or a subject for experiments) or in mercenary troops. It's no wonder that Abel goes goo gaa over petting bears or meeting aliens or fighting other people - such things are probably dreams coming true for a very young person who has barely had anything similar to a childhood or a teenagehood to begin with!
There were already some hints of Abel's more child-like and naive than one thought nature in Super SFIV, via his rival fight with Fei Long. (He's a huge Fei Long fanboy and while fighting him, he would say things like "wow, I've seen all your movies!") Since this game takes itself far less seriously than IV story-wise, it's the perfect chance to Abel's less-serious character traits and run away with them.
If Dan is stated DEAD, why is he the Tutorial trainer?
Fridge Brilliance: It's probably his ghost, brought back through the power of Pandora (the training stage is supposedly within it, according to Word of God) and maybe a little bit of the power of Saikyo.
Consider that the box grants wishes in many character endings. He's found beaten up inside the box during Blanka and Sakura's ending. The two were searching for him.
In every ending, the characters are in the Antartic; how are they not freezing to death!?
Pandora warms its surroundings? Probably explains how the characters travel to the site in a (likely insulated or heated) tank (the one that the mammoth is chasing), then head outside to claim the box.
Paul and Law's ending becomes much less funny when you realise both have been doomed drift through space, stuck in the next best thing to the Phantom Zone. You know, that thing Superman puts you in if you've been particularly naughty.
In the text-and-narrator-only Stinger to that ending, Paul and Law were "kicked back to earth" after the box was retrived by aliens, and Paul challenged said aliens to a fight, and was defeated.
Assuming "imprisonment inside the box" is the same for everyone, could Ryu and Raven have possibly been banished to this Phantom Zone-like dimension too?
Ogre's text ending tells of him returning to his home planet, where an army of countless Ogre clones are waiting. Then it is told that the data Ogre gathered on Earth will be used to strengthen this army. It's quite possible that all of the clones were sent to other planets in the universe, defeated the best that planet can offer, and returned with the planet's fighting data. So by the time Ogre returned, they possibly have the combined power of at least an entire galaxy.
Pac-Man in this game is apparently a representation of Horror Hunger. What does he do with his opponents...?