Pokémon game idea.

Truth be told I've never really been into the mystery dungeon games.

It’s always felt rather segregated, with humans being completely non-existant yet being explained that they could exist.
So this is a game I would adore to death if it existed.

A Mystery Dungeon game set in the world of trainers.

It would be set in a new region with every pokémon (up to the current generation) inhabiting it like the MD series, however with a full map incorporated into it like the main series games (not just a text based menu select of where you want to go).

Depending on what pokémon you get (there would be a quiz like normal for the people who like the randomness of the quiz and the people who don’t can use a guide to answer the questions like they usually do.) you would start residing in a different part of the region (a ground type in a dessert or a cave etc…).
You would not be a human turned into a pokémon like the other MD games but a full time pokémon, leading a completely normal pokémonic life.

You wouldn’t be able to travel far away from your starting area at first because it would be surrounded by more powerful rival pokémon which would beat you up (being KOed right now you would wake up back at your den/set/whatever home you live in). Instead you would hang around the area wandering around gathering berries, sparing with your friends, doing generic “Hey [your name here]! Get me 3 oran berries will you?” quests for the other pokémon.

When not on one of these quests you can also walk around in the grass to see if you can find any random pokémon to beat up and gain exp for. (Being a wild pokémon, you don’t get as much exp for fights, you get fractions of levels too in return for this).
Occasionally in the grass you’ll run into a trainer who is just as surprised at you jumping out at him as you are at him jumping out at you. His pokémon would be slightly stronger but not too bad at first however with every trainer you defeat or flee from they get stronger (the difficulty would ramp up quickly, much quicker than your own power gain, making it harder and harder to defeat them.)

The trainer would occasionally give lines of dialogue during the fight, letting you gauge their personality. Usually they will just fight you normally however may also try to catch you with identical mechanics to the main series games.
During the fight if you decide that you want this person as your trainer then you can fight differently to give them a higher chance of trying to catch you. (Trainers you think may be looking for powerful pokémon you can fight more aggressively to force their eye onto you, for trainers seeking companionship you could fight defensively to draw out the battle and get them to know you better, then there are trainers wanting a certain attribute (one who shouts “Go my [whatever pokémon they have out]! Batter it with your strength!” would prefer a physical attacker))

The difficulty ramping up would be to eventually force you to be captured one way or another. Eventually it would get so difficult that they just throw a master ball on turn 1, a supposed to lose fight, an you’ll be stuck with that trainer, so do make sure that you don’t just dismiss every trainer which appears.

However being caught is when the game really starts. Under a trainer you can go everywhere in the region, you can gain levels much quicker (at the same rate as the main series games), you make friends with your trainer’s other pokémon, then when your trainer wants to challenge gyms and eventually the whole league (and after that, end-game content), the also major thing you can do is evolve which you can‘t do in the wild.

You don’t actually have direct control over where your trainer takes you but eventually after you get to know him/her better you can imply things and they’ll be more inclined to do them. (Saying: “I want that leftovers item, that would help me in combat.” just after being caught would result in the reply “Sorry, don’t understand you. What do you mean?” if you’re loyal and obedient would result in the reply “You want.. Umm.. This leftovers? Yes? Sure! Here you go.” if you’re rebellious and not nice (disobeying orders to use moves, arguing with the other pokémon in your party, things like that) then you’d get “Hey! You can’t have that!”)

Things you’d have limited control over would be the items he gives you, the food he gives you, general direction of where to head towards next, which moves he teaches you, which gym battles or contests to attend and things like that.

You could also get your trainer to release you depending on what they want of you and not fulfilling it anymore if you’ve gone for being a disobedient prankster, or simply by appealing to them if you’re a loyal obedient pokémon. In which case you are wild again and your new starting area is the area he released you. You’ll wake up there if you’re KOed. The trainer difficulty gets reset back to 0 as well. So you don’t immediately get recaptured after just being released.

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That's my idea for a game I'd drool over if it came out.
Although I haven't decided if it would be best suited to be an isometric game like MD or a turn based one like the main series. Maybe it would switch when you were under command of a trainer and when you were wild or your trainer let you out to play.

Interesting as it sounds, this doesn't sound terribly fun to me. It'd be like being a virtual pet in reverse, or something to that effect. One major problem is that you'd better be able to "influence" your trainer to pick out some decent teammates for you. Because otherwise, what are you supposed to do when you get to a Gym Leader with a good type matchup against you?

Then there's the matter of scope. As you said, you'd be controlling one Pokemon... but you'd -have- to be captured at some point. One major problem there: this means that you're -not- the starter Pokemon. Therefore:
1. There's no good excuse for why you wouldn't be in a ball the majority of the time. Not a lot you can do from there.
2. The trainer has at least one other Pokemon besides you. What exactly are you supposed to do while he's using the other Pokemon? Again, you can't really give any input from in the ball.
3. Assuming you're outside the ball, there's problems with influencing the trainer's battle decisions. If you make -all- the decisions for him, why bother not playing a regular Pokemon game? If you don't make any, better hope the AI is decent.
4. "You got stuck in a computer forever. Game over."

Also, why exactly can't you evolve in the wild? Trading is one matter, but... as far as I can tell, leveling up is still going to happen here, just a bit more slowly. And I don't see any good reason why you wouldn't be able to find any applicable evolution stones.

For that matter, there doesn't seem to be much of a goal here. "Screw around until you get captured. Help the trainer until you force or beg him to release you. Repeat forever." Not that I have a problem with sandbox-type games, but... if it's going to be that, let it BE that. If there's no particular objective to get done, don't have it FORCE you to get captured at some point or something. Sure, you can let yourself get captured if you want to. And you can get captured anyway because that's how game mechanics work, but it's alright because you can essentially leave via two opposite and fairly easy means. It just seems kinda arbitrary and forced to have a mechanic like "you've fought X trainers without getting caught, so trainer X+1 will have a Master Ball because we're forcing you to get caught eventually."

I understand that getting caught essentially promotes your growth, but you shouldn't HAVE to do it. There should be other things to do. And again, the matter of "things to do." I'm 90% certain that, as a wild Pokemon, you aren't gonna be all like "Someday, I'm gonna beat the Pokemon league!" That's the trainer's goal.

So, long story short: interesting concept, but it seems kinda unfun to be on the pet side of a virtual pet game, and spiking the difficulty up to force a player to take a certain path is extremely... I dunno, it doesn't suit this unless there's gonna be an actual story in mind. And this doesn't really seem like it does. It'd be like playing Minecraft, and getting "There's a gigantic world to explore, but if you go any direction but north you'll be swarmed by armies of creepers because you need to go north first." You're a wild Pokemon, and can pretty much do whatever you want provided your abilities allow it! But you have to get captured. Not a matter of "statistically it's probably going to happen eventually," but a matter of "it WILL happen arbitrarily if you avoid it long enough." Kinda kills the openness of your objectives, so to speak.

Okay, that wasn't short. I'm sorry, I didn't get a lot of sleep last night and that tends to make me rattle on and on about things.

One last thing: I don't really think it'd play like either a PMD game or a main series game, personally. I'm thinking eastern RPG, but with the decision-making (the trainer, in this case) relegated to an NPC instead of the player. Incidentally, double battles would be a LOT more fun on this than single battles. Or at least interesting. Think the multi-battles on the main game; you're on a team with someone, but don't quite always know what they're doing. Compare to a regular double battle, where you command your entire team. It kinda gives more of a sense of actual cooperation, since you have to work -with- someone. (Besides, double/triple battles would be a decent excuse for your character to always get used)

One last last thing: I agree on the PMD lack of humans thing. The fact that there's quite a few Pokemon that are notably the result of human intervention or technology (Porygon, Trubbish, Grimer, Voltorb, Magneton, Castform...) and others that rely on humans for whatever their sustenance is (notably electric types that feed on electricity)... kinda makes the no humans thing make not much sense.

Well the aim of the game would to to be captured rather than to not be captured. The difficulty wouldn't spike, the easiness would.

As for the combat mechanics, your trainer would tell you to use a move then you'd have the choice to do it or to use a different move. The one he said to use would get a bonus in accuracy while if you think that you should use a different one then you do that. (Think of how when a CPU uses sing it seems to always hit. Well if your trainer says to use it this turn it'll have 90% accuracy instead of the regular one.) Although the way you fight influences the way the people around you act towards you, and if you refuse his orders then they'll be normal accuracy however if your gambit pays off then I'm sure your trainer will be prepared to forgive you, (which if it pays off a lot of time then he may trust you own judgement more which won't damage your standing with him).
That said the CPU will mostly be right.

As for the pokéball: When you're inside it, time doesn't pass, there's a short animation of you sleeping for about 3 seconds then you're released.
During fights you are outside the ball at all times even when switched out, watching its progress.
There's no PC, and when caught you're always directly on the team.

And as for the Goal: There would be one.
I didn't really get as far as a plot in my thinking however there could be something following the main series games. Something like a villainous team which you and your trainer have to fight.

And finally there could be a standard pattern for things.
Wild: Same as MD.
Caught: 1.) Get caught
2.) A few wild battles
3.) A trainer battle or two
4.) Get to the next town
5.) Get let out to go off on your own for a bit and do things
6.) Gym battle (lots of trainer battles then a gym leader who's even stronger)
7.) Set out towards next town.
8.) Repeat from #2