Omnilium, Summoning, and Science.

[Amaterasu]

A loooot of stuff is in here, but you need to separate "in-universe" elements such as the inability to use flying mounts in some verses, but then you can in others, and the "metagame" elements which serve to balance the game as a whole so that Superman and Goku don't auto-win every fight.
I'll just separate those two to make the discussion easier to follow.

DISCLAIMER:
These are things "as far as the Primes know", which may be mistaken. I also bring in a lot of my personal findings, which may be incorrect.

Metagame elements

• OM as a number is a way to quantify the amount of Omnilium you have. Just as you can't say "I have one water", you can't say (in-universe) "I have one Omnilium."
  
• Any character can summon anything within certain limitations (such as not pulling characters from unrelated media), limited only by their imagination. Some imaginative Spartan could think of a "sword made out of glowy light" and summon a lightsaber.
  
• 3+ minutes is mainly a metagame rule, explained in-character by "Your character must concentrate, visualize the item etc." but it is also there to prevent pulling solutions out of your ass and other imbalance issues like instantly summoning a car while fleeing a battle, and driving away. Things such as moves that summon items are more of a "supernatural power" than Omnilium summoning, and fall under a different restriction.
  
• The balancing of moves is completely and entirely a metagame element. If Camelot didn't have magic their weapons would be weaker than Coruscant's because they are not as technologically advanced, for instance. This is to keep people from having a "home advantage" by picking the strongest possible character and dominating the entire game just because of that.
  
• The number of secondaries is a metagame element to prevent people from raising armies out of nowhere. If it was an in-universe element Palpatine, Aragorn and Diablo would have armies of a couple dozens of guys. That'd be underwhelming.
  
• The OM cost of "mechanical benefits" is to limit your character's ability to obtain advantages through the amount of OM that you have. Otherwise it would be no use having a currency implemented.
  
• The costs of things are a metagame element that cannot be quantified in-universe. Otherwise, why would five cellphones (Communicators) cost the same as a mansion and a small village (a Base)?
  
• OM gain is independant of the actions of your character (walking around for 100 words or Omnilium extracting for 100 words is worth the same OM). To compensate, hand-waving exists.
  
• Time dilation is a way for the site to explain how despite different speeds that one or another thread may progress and thus different Primes may perceive time differently, there is still one continuum. The only measure that we have is real-world time. We are NOT allowed to use time dilation to fast-forward the time faster than it passes in the real world (you are not allowed to have your character do a 10 day IC trip in 5 days OOC time - correct me if I'm wrong on this).
  

In-Universe elements: As far as we know, anyway.

• Everything in the Omniverse is made out of Omnilium. Primes, Secondaries, the environment etc.
  
• Omnilium is both matter and energy.
  
• Summoning anything costs Omnilium, extracting Omnilium from anything gives it to you. Even if those gains and losses are hand-waved (they don't count towards your Spent OM), in-character your character gains or loses some Omnilium.
  
• If you "run out" of Omnilium your character would simply not be able to finish what they started. If Omnilium is lego bricks you can build with them until you run out, but you can't have a negative amount of lego bricks in your box because you used more than you had.
  
• The abilities that distinguish Primes from Secondaries are the ability to manipulate Omnilium, and the ability to respawn upon death. I believe that Primes carry their Omnilium with them at all times, and slowly absorb more subconsciously (gaining OM even when your post is about your character picking their nose for 10 minutes). Perhaps it is a "trade" with Omni, or perhaps they really transform an amount of Omnilium into an object or creature.
  
• Magic is just one form of force - ki, chakra, mana, Ember, whatever you want to call it, they all fall under that umbrella.
  
• Elemental advantages ("Fire is weak to water") exist in-universe. We are just not allowed to exploit them for an unfair advantage in battles.
  
• "Our characters know how to use Omnilium innately" Well I mean, it ain't rocket science to visualize an item in your head. And Omni explains it in the Intro. (he may have messed with our heads tho).
  

EDIT:
Omni has noted that a lot of the stuff said in here is wrong. Don't read too much into it until he responds and corrects me.