Disclaimer: This isn't meant to offend anybody who is content with how Pokemon is now, nor is it meant to question your tastes in gaming. This is just my perspective, one that I feel I am not alone in. A lot of my ideas just scratch the surface in terms of gameplay. I am not a developer so nitpicking is irrelevant; its just an idea to draw upon.
I was 11 years old when Pokemon first came out and like many I was swept up in the craze. Throughout the years I have enjoyed almost one Pokemon game from every new generation, with the last Pokemon game I played being Diamond. Since then I guess I just grew out of it. But over the last couple years I began seeing the franchise in a different light; how there are so many seemingly adult themes such as slavery and animal cruelty that Nintendo has (IMO stubbornly) strictly tried to maintain a family friendly look/tone.
I am certain that Nintendo will continue the route they have taken with Pokemon so far. I hope Microsoft and Sony see the potential and try their own take on Pokemon, but with a more mature tone to them to please the adult gamers who have since grown out of traditional Pokemon. Because the demand is there, of that I am certain. These are just some ideas that I have if a more mature version of Pokemon were to be made.
1. Make a full blown console game.
Make a gorgeous, 1080p game worthy of being called a next generation Pokemon title. Max out all the space on the disk to make a georgeous polygon heavy, breathing world that just begs to be explored. Make the user able to walk freely and not just the 4 main directions of a compass. With a console game comes a richer online experience and options to choose from. Battle a friend, quick matches with whoever is online, doubles modes, abilities to customize rules for battles such as "no legendaries, only certain generations can be used, no held items, Type restrictions, etc.....the possibilities would be amazing to battle exactly how you want. Trading could be even more of a ease. I think this would be any Pokemon fans wet dream and would definately bring back the older fans who have since lost the connection to the franchise.
2. Serious Looking Pokemon.
There is an un-godly amount of realistic Pokemon fan art. People want it. To me, it takes away the joy of controlling a menacing ghost or a fire breathing dragon if they look non-threatening to a kingergardner. The most fearsome looking pokemon are for the lack of a better word "kiddied up" to have that "E For Everyone" stamp. For once I would like to have a Pokemon look as badass and intimidating as it should.
3. Address the Mature Themes, Make Them Affect Gameplay.
Being 10 years Old/Story:
Being 10 years old and leaving home just cries out child neglect and bad parenting. No parent would let a child even own a pet without supervision at age 10. Make the trainer 21. He/she is older, mature, an ADULT. And its easier to bear the thought of a adult controlling a legendary pokemon rather then said legendary pokemon being beaten to a pulp by a 10 year old.
The story should also be given a more mature tone. I see nothing wrong with being a trainer because you enjoy the thrill of battling and the money is lucrative. This is your motivation at first. But as you inevitably deal with a terrorist organization like Team Rocket/Magma/whatever, you soon develop a conscience to make it your business to stop them. Maybe their actions injure a friend or loved one and sets you on the path for revenge? The possibilites are many.
"Fainting", Consequences, and Healing:
A lv. 100 Charizard uses fire blast on a lv. 3 Pidgey.........it faints. The game should calculate certain things like level gaps to determine if an attack is considered "overkill". If an attack just manages to deplete a Pokemons health, it faints. If the attack was so strong that it would have fainted the Pokemon 2 times over, then it should die.
In that case, this teaches the trainer to be wise about their actions when dealing with a random battle or with a trainer.....to basically flee or just give the appropriate amount of effort, not to overdo it. Killing a random Pokemon would have you fined. Killing a trainers Pokemon would have a much bigger fine. A Mass Effect Paragon/Renegade thing could come into play here, where people talk to you differently based on your actions (and severity) in battles.
When it comes to healing, the same thing would apply to you. Your Pokemon could also die if an attack could faint them 2 times over. This teaches you to pick your battles. If just hurt, a Pokemon center should heal instantly like in the games. When it comes to fainting however, it should take actual time to heal your Pokemon. You shouldn't treat your Pokemon with such disregard. If they faint, you deserve to pay the inconvienent consequences of your actions. Let's say it would take a Pokemon center 10 real minutes to heal a fainted Pokemon. I would say that is real incentive to not charge blindly into the next trainers battle. A similar thing would apply if your Pokemon is burned, frozen, etc. where you would have to pay an extra small fine to heal them.
Slavery/Animal cruelty/Make Pokemon Battling Looked Down Upon, Yet Legal:
The game says trainers share a love with their Pokemon and that their Pokemon love them. Would you send your pet cat or dog to battle with another kids pet until one or the other loses consciousness? And even if you win, your pet would be most likely badly injured? No caring person would do such a thing.
Which is why the trainer should have a grittier outlook on life to warrant his actions. Make the Pokemon crave the battle, have respect for the trainer but have no real affection for them. Also, make Pokemon battling like smoking in the societal sense: legal, yet almost everybody looks down upon it. Trainer battles would take place at night or in private areas to avoid criticism and protest. Pokemon "Gyms" should be viewed as an underground organized crime where people take bets on your battles with the leader and you gain a badge as a form of street cred to carry over to the next town with a "Gym".
When you capture a Pokemon, they are initially scared and resentful of you, as they should be. For the next 5 battles, random or trainer, they will disobey your orders and use a random attack of their own choosing as a means to defend itself, not because you ordered them to. Eventually, they will see that following your orders is the best way to guarantee getting out of battles alive. They won't love you, but come to respect you for your resolve and tactics.
Make Battles Fair:
A random trainer has 2 pokemon in their belt. You have 6. You can use all 6 if you so choose to. How is that fair? Before every trainer battle, you see how many Pokemon they will use and you can only therefore battle with that same amount of Pokemon. Trainer has 2 Pokemon and beats your 2 Pokemon. You have 4 left. Doesn't matter. You lost the battle and have to pay the losers fee. This would make every trainer battle taken more seriously.
Side Note: Take away PC for storage. Your extra Pokemon would starve and die. The solution: your origional home is a farm. You essentially "ship" your Pokemon back home so at least you can see them and they are free to move.
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Just my thoughts on a more mature Pokemon game. Notice how I said no blood.....a mature game doesn't need blood, just mature themes. Let me know what you think.