MST3K Mantra: Let's all remember what the mantra is:
While part of the mantra is telling you that you shouldn't be thinking too hard on little details as those details are ignored in-universe just to keep what you're watching/playing moving forward, it's also telling you not to take things so seriously. I think it's perfectly fine to speculate, but don't take it seriously like you're going to win an award or something. If you have a fun theory that makes sense (at least to you) then post it, the worst thing (well, reasonably the worst thing) is that someone says they don't agree and points out some of the problems with the theory (which you can then maybe use to help shape your theory). And if someone is more volatile toward your theory then its them that needs the MST3K Mantra, not you.
I posted plenty of crazy theories (most having to do with Pokemon being able to manipulate energy, but hey once you open that can of worms the question of what can you do with it comes into play), but I'm not against other's theory and like to hear what people have to say. For example:
I'm not saying it has to match the animation. I can't see anyone on top of a Pidgey (I always imagine that smaller Pokémon grabs your shirt with its feet).
Now while I still like my theory, this one makes perfect sense too. We need to remember Pokemon are eldritch abominations in "acceptable" forms. Because he's right, if they put enough strength an energy behind them a small Pokemon can probably lift and carry a person someplace else. Do you know Rufflet can learn Sky Drop? How many "weak" Pokemon can learn Strength? There are a few small Pokemon who can (or were) able to learn Seismic Toss. When a Pokemon puts their mind to it they can do things you don't think they should be able to do.
Or if the idea still bothers you, just take it as a game mechanic. Why can the small bird you can easily catch able to fly your across the map? Because you can easily catch it. Fly is primarily meant to be a quick travel tool and they don't want you looking around for/training up a Pokemon which logically would be able to carry you on its back. There is a divergence in pure game mechanic and in-universe physics. So you can either accept these little theories, or just shrug it off as the game creators not wanting to bog you down.
Yanmega Isn't A Fly: Yanmega is a dragonfly... wait my joke still doesn't work, DARN IT! Anyway, why can't Yanmega and the majority of flying Bug-type Pokemon learn Fly? Hmm, that is a good question. Anything I can come up with will have logical holes:
Maybe because Bug-types that can fly can't fly for long distances without needing to take a break? Well then why can some participate in Sky Battles and how come smaller, weaker, and inexperience Pokemon still able to fly just fine?
Maybe their wings aren't made to exactly carry something for long distances. Once again, the small and weak Pokemon who don't even have fully developed wings are able to carry you just fine.
They can't remember landmarks? But you're directing them.
They don't take directions? They don't have a problem listening to you in battle.
Their insect minds has them fly in a certain way (ever watch a bug fly, they go all over the place like they have no idea where they're going) that isn't suitable for having them fly you someplace?
Hmm, actually I like that last one, though it does sort of overlap with how can they obey you in battle perfectly if their insect minds process things differently. *shrugs*
NEW MYSTERY:
This sort of has to do with how Pokemon Origins displayed something. We all know about Cubone's mother, Marowak who we later face as a ghost in Pokemon Tower, was killed by Team Rocket. I always thought it was killed with Team Rocket were maybe escaping someplace and they used a gun or an explosive to get it out of their way. However, in Pokemon Origins it shows they were just poaching Pokemon as usual (with nets and stun batons), a Rocket Grunt wanted the Cubone because they were rare and sold for a lot, and mother Marowak stood in their way so the Rocket Grunt killed it with a stun baton as the child Cubone watched from a distance.
Some questions about this:
1. How did a Rocket Grunt kill Marowak, a GROUND-type, with an electrified stun baton (and it was an electrified one, you say it spark)?
2. Did Marowak just stand there and let the Rocket Grunt hit it to death? You don't see the Rocket Grunt tangle it up in a net, he just WALKS UP TO IT. Why didn't Marowak beat the mulch out of the guy? It's not a Slowpoke, its a Pokemon who can actively fight and uses a bone for a club!
3. If Cubone are so rare, why did the Rocket Grunt let it get away. Not only did it not run away far, there were also other Rocket Grunts and they had nets. So they killed the Marowak... and let the reason they killed the Marowak go?
4. Why kill the Marowak? If Cubone are so rare, why not capture the Marowak and have it breed more Cubone? Heck, if Cubone are so rare than Marowak are probably even more rare so you probably could have sold it. Once again, you had nets.
5. Why are you even using nets? Just use Pokeballs, less struggling and easier to carry them. You only need nets if you're going to capture trainer's Pokemon if you can't just beat the trainer up. Or at least use Pokeballs with nets, like have the nets do damage until their weak enough to capture in a Pokeball.