Bokurano/WMG

Reincarnation is true, and the system is a natural/divine phenomena to recycle souls.
If reincarnation is real, and a soul cannot be created from nothing, then there should be some finite number of souls sitting in the afterlife waiting to be reincarnated, and that number will go down as the population grows. The destruction of alternate realities is a means to actually merge theirs with ours and bring all their souls into our afterlife (this guarantees we will never run out of souls because there are an infinite number of alternate realities). Why robot battles piloted by the residents? because the people of said universe deserve to be the deciding factor in the outcome. There is no real evidence to support this but in the manga they do bring up reincarnation at one point, and they also speculate that the events are somehow just a natural phenomena beyond their comprehension.
 * So if there's an infinite number of alternate realities wouldn't that mean an infinite number of souls?

The humans who run the game are Straw Anti-Spirals
Anti-spirals destroy planets with large numbers of Spiral beings so that the amount of mass created by Spiral Energy doesn't cause the universe to be destroyed in a Big Crunch. The people who run the game destroy universes for no adequately explained reason.
 * The games take place in order to weed out all of the parallel worlds because of something akin to the Spiral Nemesis happening. If too many parallel universes are created, then a Big Crunch would be created from all the universes. If anything, these games are used by the Anti-Spirals themselves to make their enemies fight against one another and prevent an uprising, as well as some form of gladitorial entertainment. The worlds which go completely undefeated in the games are probably then monitored closely by the Anti-Spirals, and Human Annihilation Devices are probably placed on the worlds considering these worlds have a great abundance of Spiral Power already.
 * I smell a plot for Gurren Lagann & Bokurano's Super Robot Wars debut...

Alternately, the humans who run the game are a unique form of Spiral Nemesis.
They are Spiral beings that found a way to destroy energy, as well as create it. At some point they decided that they were superior to all other beings in the multiverse and created the game as an entertaining way to eliminate lesser beings. When someone loses the game all matter in his/her universe is destroyed, but the universe itself remains intact. The humans who run the game then send a small group to use Spiral Energy to create new matter and colonize that universe.

At the end of the 48-hour period, nothing happens
Consider it. So far, we know that killing the pilot results in the death of the universe; but we've never seen a 48 hour period end, with good cause. The truth is that the end of the 48-hour period means that nothing will happen and there is no need to fight.

It's a sadistic answer to a sadistic manga.
 * A strange game. The only winning move is not to play
 * ... that's the second time today I heard someone use that quote about this series.

The branching point between alternate realities is the point where the people behind the game send the robots over.
Just because the storyline isn't quite horrible enough until you make it a Shoot the Shaggy Dog plot.
 * Um... I feel stupid. What are you saying?
 * Alternate realities wouldn't exist if the people behind the game didn't send the robots over in the first place.
 * If new alternate realities branch every time robots are sent over, that means that the total number of alternate realities is constantly increasing, even if most of the new branches get destroyed after losing a round.
 * Really? The why I see it, the new branches are (relatively) instantly purged, since whenever a new branch is created the two current branches fight and one of them is wiped from existence.
 * I think it's been disproven by Tanaka and Seki not recognizing the planes in the other world. So at least some branching points are some time in the past.

Dr. Manhattan is behind all of this
He created all alternate realities and make them fight until only one will survive. You have to admit he could do this.

The kids are in Hell
All this is just a vast Mind Screw by Satan and the other demons. They're just putting an elaborate psychoilogical horror, isolating them, and dumping upon them the vast guilt of murdering over a dozen realities, with the alternative dooming their own.

The game is all for the purpose of collecting immortal souls
The demons or whatever is behind the game can destroy universes with ease but what they really want is to gain possession of souls, preferably children's innocent souls. However the demons are bound by God to strict laws that allow them to take someone's soul only if a) that person explicitly agrees to a deal, and b) the demons fulfill their end of the deal first, and c) the person accepts the benefits. The loophole is that the demons don't need to tell contractees what they are selling or that immortal souls even exist.

The destroying universes part is because parallel universes are dime a dozen and threatening their destruction is a great motivational tool. The giant robots are used because the demons like collateral damage and because the pilot dropping dead, soul taken, a short time after winning is easy to pass as having been due to the strain of piloting.

The game was created by The Nameless One
TNO created the game, which pits entire universes against each other and is slowly causing the multiverse to die (Koyomeshi lied about it being a necessary "pruning"; it's really done For the Evulz or some other unjustifiable reason). It was a crime so heinous that he sought immortality to avoid the richly-deserved eternal consequences. The game kept on going long after he had forgotten about it (due to being reincarnated). The most powerful shadows are the spirits of deceased pilots who have been placed in forced servitude to The Transcendent One.


 * To add to the above: recall the symbol that's found all over the place in the Fortress of Regrets. In it's centre, there are two serpentine lines reaching towards the same goal, however only one reaches it and the second withers and falls away. Perhaps it represents the duels between universes.

The Earth is a simulation, and the game is an evolutionary algorithm for creating strong-willed AI.
The game canonically fits every real-world criterion for being an evolutionary algorithm: it has both mutation and selection. Selection is based on how well a random sample of children can fight, and the biggest impediment to fighting well is not being able to deal with the psychological trauma of the task. The young age of the pilots and a sadistic guide ensure that the pilots experience as much trauma as possible, to make sure that it's the dominant selection pressure. The Zearth Program is a trap to stop humans from reverse-engineering Zearth. As the game goes on, the Earths that survive tend to be the ones with more resilient humans.

The Masterminds are ultimately benevolent humans that have advanced far enough to create strong artificial intelligence, and they're trying to make a better human. (After all, from what we've seen of them, they appear to be humans, and it's more plausible for humans to have that kind of power in virtual universes they've created than in other "real" ones.) Unfortunately, either they don't understand the ethical problems, they think Utopia Justifies the Means, or they're just looking for money or power (probably the latter, given the show's themes). Alternatively, they understand exactly what they're doing, but their own world is in danger of destruction, and creating advanced AI through the algorithm is the only way they have to save it.

The Earth is real, and the game is an evolutionary algorithm for creating strong-willed humans for the Masterminds to feed off of.
As above, but the Masterminds are malevolent, god-like beings. And they're hungry. Strong-willed humans have the tastiest or most filling life energy.
 * The masters are the C'tan? Or maybe the chaos gods?

In the anime continuity, Maki had a crush on Waku.
She's a Tsundere who only shows her "Tsuntsun" side to Jun (becaue he abuses his sister) and Waku. If, they would have eventually formed a Slap Slap Kiss relationship with each other or at least have had some Slap Slap Kiss-themed ship teasing. Also, Waku was built up as the team leader. Maki's Team Mom tendencies and Action Girl nature would have made her a natural second-in-command. The Battle Couple that never was, indeed.

Kodama is a descendant of Johan Liebert.
And the apple doesn't fall too far from the tree.

The game is a system for the creation of an optimized combat mecha.
The idea of determining which of a series of existences is most deserving by which has the best pilot and robot makes little sense. However, because the survivors are determined by the outcome of a fight, it makes sense that the most deserving mecha survives. Given that everything is, on a fundamental level, information and that there are an infinite number of alternate worlds, such a testing system would require almost zero expenditure of limited resources. All that would be needed is a method of inserting the blueprints into the operational theaters, a method of forcing combat, and a method of identifying the winner. The destruction of the loser's world is both of the latter methods. By allowing a world to 'win' by accumulating 15 victories and then passing it's mecha onwards, no world has the time needed to delve too deeply into the game or the functionality of the mecha. When a set number of mecha were left, the game would end and the winning designs would be further refined for the next test.

The story is a metaphor for growing up.
Just listen to the lyrics of Uninstall with that mindset. You should see what I mean.

Koyemshi lied in the anime: the last pilot doesn't survive the demo fight
Koyemshi is not only known for torturing little children and killing kitties for fun, but also for blatantly hiding information and outright refusing to fulfill some of the rules until the kids learn of them. This may also apply to the last pilot's fate. Think about it: Even if Kokopelli. Since he has the masterminds and the gray beetle watching over his actions, the second option is highly improbable. He also lied to Jun, then:. Why did  didn't call him out on that? Simple: it was better if the pilots had hopes of surviving so they would give all they've got and save their world in the demo fight, assuming that the "if you lose on the demo fight, your world is destroyed instead of the new contractees' one" rule applies on the anime. The gray beetle, though politer, is suggested to be as sadistic, if not more than Koyemshi, so the whole deal was either her idea of breaking down Koyemshi's will at the time, or just Koyemshi trying to look like the "poor little guy" instead of the "little bastard who cried so badly he got what he wanted". Not that it worked, though.

The anime is in fact a big Russian Reversal.
Because GAME UNINSTALLS YOU!

Our universe wasn't the perspective universe.
The direct analogue of our universe was one of the fifteen universes whose pilots were defeated by Zearth. Our Earth was destroyed without even a passing mention. It seems fitting, even though there's nothing to suggest that it's true.

The game is a sort of anti-Sburb
One destroys alternate universe, the other creates them. IT'S ALL SO SIMPLE.