Ah, the child Prodigy theory. Yes, I like that one too. And I also believe it is why you're taken out of school to pursue a Pokémon training career full-time (we meet many trainers standing in one spot all the time, presumably they're just there on a hobby basis), and how you're able to use Poké Centers for free - your mom or the professor sponsor an unlimited-use subscription for you. You may even get corporate sponsors eventually - which enables your mother to stay at home all day: as your legal guardian, that money is also hers until you turn 18.
(And PokeMart Discount Theory)
I also go by the child prodigy theory. That said not to sure about some of the ideas you suggested:
Taken Out Of School: Honestly I kind of question exactly what the education system is like in the Pokemon World. It can't be like ours where kids are expected to attend school until they graduate high school and move onto a career or college. No, it seems like in the Pokemon World your taught the basic stuff at a young age and when you finally reach your teens more options open up. Now for the player it's going on a Pokemon journey, however besides that we don't actually see kids our age going to school. The most we see are apprenticeships or continuing a family business. Now there's obviously scientists and professors so there does seem like a route for higher education if someone wants to go down that route, but an education route doesn't look like the only option teens in the Pokemon world have.
Free Healing & Low Mart Costs: I don't want to get political here, but it feels like Pokemon world sort of has a loose form of a welfare state. All trainers have free healing for their Pokemon, Marts sell all the supplies they need at a low cost, and the Pokemon League (a possible branch of the government) funds them. Of course there has to be money making somewhere and I can only think of one way its done:
MERCHANDISING! Pokemon Training is super popular as well as activities connected to it (battling, Contests, Pokeathlon, Musicals, PokeStar Studio films, etc.). They air all that stuff on TV which makes people then want to go out and buy Pokemon merchandise. Of course you need Pokemon Trainers to be able to do any of this and, let's be honest, being a trainer isn't exactly a high paying job. So, in order to make money selling merchandise, they make healing free (and keep costs of being a trainer low) so that they can participate in activities that businesses can show and sell merchandise off of. And yes, you don't see a single cent of it, capitalism at its finest!
What About Mother: Not sure if your mother sees any money from this, even if their kid does become famous. In addition to being a prodigy, it also feels like the player is from a well off family. Your mother seemingly doesn't need to work, all of them appear to be house wives where your father is the breadwinner. Though the only games that show this is Gen III where your father is a Gym Leader. Maybe at most the Professor's Lab is giving your mother money since you're filling the Pokedex for them. Also after becoming a Champion you probably are given money making opportunities after the point the game ends that helps the player continue their Pokemon training career and support their family.
I like the theory floating around that RBY Giovanni is actually trying to save the world from Mewtwo.
Well, I would certainly agree it's plausible that Giovanni would be trying to get the Silph Scope and Master Ball all in an attempt to capture Mewtwo... but it wouldn't be for saving the world. It would be because it's a powerful Pokemon he'd have under his control and no one would be able to stand against him, something a crime lord would like to have. I'd question if he would try taking over the world... though we know at least of two versions of Giovanni who would (anime's and Rainbow Rocket's).
Also getting those two items serve additional purposes:
Silph Scope: Team Rocket were keeping Mr. Fuji hostage in the Pokemon Tower, and the only way to get up to them was using the Silph Scope to identify Marowak's Ghost and defeat it. But why is Team Rocket keeping him hostage? All we're told is that Mr. Fuji got angry they killed Marowak and went to give them a peace of his mind, but why wouldn't Team Rocket just push him back if that's all he did? And why seemingly go out of there way to prevent him from getting rescued? Well, we know Mr. Fuji is the lead scientist who created Mewtwo, so if Giovanni is looking for Mewtwo who better to "interrogate" then the one who created it? Mr. Fuji didn't tell you that part because he wants to keep Mewtwo's existence a secret.
Master Ball: A Poke Ball that captures any Pokemon 100%. Could you imagine the Pokemon force that someone could build up by just searching for rare and powerful Pokemon and catching them with no effort? Giovanni can, and he would have the resources needed to make more Master Balls and the manpower to send groups looking for rare and powerful Pokemon. Sure he'll have Mewtwo at his beck and call, but he's still just one man and he knows to get anything done you need an army of loyal servants and they'll need strong Pokemon to enforce your will.
I posted about this one years ago I believe, but I still enjoy it: I like to think that the reason so many of the Gen 5 mons evolve late is that it's a very subtle jab at American culture being rather conservative, with Unova being based on the US and all. That's probably not true, but it's fun to think about.
Actually it's because you catch those specific Pokemon so late in BW that those levels don't seem ridiculous there:
Vanillite (35 to Vanillish, 47 to Vanilluxe): Earliest you can catch a Vanillite is at Cold Storage at level 20-23. From there you need to wait 15 levels to evolve it to Vanillish and then 12 for Vanilluxe. This is about the same amount of levels for evolving your Starter.
Klink (38 to Klang, 49 to Klingklang): Earliest is Chargestone Cave at level 25-27. You need to wait 12 levels for Klang and then 11 for Klinklang. This is a shorter amount of levels for evolving your Starter.
Axew (38 to Fraxure, 49 to Haxorus): Earliest is at Mistralton Cave at level 30-31. You need to wait 8 levels for Fraxure and then 11 for Haxorus. This is a shorter amount of levels for evolving your Starter.
Deino (50 for Zweilous, 64 for Hydreigon): Earliest is at Victory Road at level 38-40. You need to wait 12 levels for Fraxure and then 14 for Haxorus. This is about the same amount of levels for evolving your Starter.
Mienfoo (50 for Meinshao): Earliest is Dragonspiral Tower at level 30-33. You need to wait 20 levels. That's the same amount of levels you need to wait for the rodent Pokemon like Ratatta to evolve.
Pawniard (52 for Bisharp): Earliest is Route 9 at level 31-34. You need to wait 21 levels. That's just a bit longer than you need for evolve the rodent Pokemon.
Rufflet & Vullaby (both evolve at level 54): Earliest is Route 10 at level 34-36. You need to wait 20 levels. Same amount of levels for rodent Pokemon.
ONLY exception to this is Larvesta who has a ridiculous 59 level wait and you get it as an Egg! However you can catch a Volcarona in Relic Castle that is level 70.
But yeah, they weren't making a jab at American culture of anything, they were actually being good game designers. HOWEVER they then went to being bad game designers by not re-adjusting the levels yet allowed you to get some of these Pokemon earlier thus making the waiting time feel long.
NEW THEORIES:
Emma Is A Member Of A Dragon Clan: For those who don't remember Emma, she's the street urchin that Looker begins looking after in XY who later becomes Essentia. While we don't know her for long we do know a few things about her like she's physically strong (having beat up and became the unofficial leader of the Lumiose City street gang), is able to communicate well with Pokemon, and has a dark skin tone. These characteristics are very similar to two other characters: Iris and Zinnia. Physically strong (at least for Zinnia), communicates well with Pokemon, and are dark skinned. Both Iris and Zinnia are from a clan of people who raise Dragon-type Pokemon. So, it could be that Emma is maybe also from a Dragon Clan.
"Well, that really didn't go anywhere"
Yeah, it's a rather weak theory, especially since it's from another wild theory I had but was debunked upon doing research: Emma was Zinnia's daughter. Assuming ORAS's place didn't change in the timeline, Gen III and Gen VI are 10+ years apart. And being how big a f***-up that Zinnia is, maybe she had a child in a relationship that didn't work out and, not knowing what to do, abandoned the child and ran away. Would explain why so many of Emma's traits match Zinnia's. "So, what's wrong with the theory?". Well, as it turns out Emma is 16 in XY. The only way for this theory to work is that, immediately after the events in ORAS, she would have to go to Kalos and get knocked-up. And even then that's still an EXTREMELY tight range of time for all of that to happen. Had Emma been younger it might have been possible, but at age 16 I think it makes Emma too old for this to be a reasonable possibility.
Zinnia Was Going To Commit Suicide: Speaking of Zinnia, another one which I think we've pointed out before. Now there's been some other "this character committed suicide" theories like Giovanni in HGSS, however I feel there's some plausibility to this one. During the climax of the Delta Episode, we're chosen by Rayquaza to ride into space and destroy the meteor by Mega Evolving it. Luckily we had this spiffy high pressure suit (that also must have an oxygen supply) we can wear as we launch off into space. However, according to Zinnia's plans, it was supposed to be her that went with Rayquaza into space... and she DOESN'T have a spiffy high pressure suit.
Now, there are some workarounds to this, the most obvious one being Zinnia was planning on using the player's high pressure suit. But, considering how Zinnia was acting during her story about Aster... it does sound like Zinnia is suffering from depression or trauma and may very well have decided that in addition to saving the world she'll also give up her life so she could be with Aster once again. Luckily the player was chosen instead of her, sparing her life and letting her speak with her grandmother to get a new lease on life.
Rui Can Use Aura: Going to a happier note, a simple theory. Rui, the companion in the first Colosseum game, has the special ability to see the dark aura surrounding Shadow Pokemon. An odd power to have, until Gen IV introduced the concept of an Aura Guardian and the mystical power of aura. And this is something in the games as Riley's Platinum sprite does show him using aura. So, could it be that Rui may be able to use aura? She can already see aura like a Riolu can.
That's all for now.