This post turned out longer then I expected it to, so there's a summary at the bottom.
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This is usually the attitude that takes a game and runs it straight into the ground. No offense to your ideas, they are great ideas that work in games, but if implemented into Pokemon they wouldn't be as cool as you think they'd be. Plus, most of your ideas aren't even innovative, they're methods other games use quite commonly and for one I'm very happy Gamefreak haven't taken some of them on.
To start, I agree whole heartedly to this post on page 1.
Plinglebob said:
3) Of course you're being ignored. By being 24 and still playing Pokemon (for reference, I'm 26 and still have my original imported Pokemon Red cart) you are the very definition of a "Perifery Demographic" like the adults who collect Barbie dolls. The point of each generation of Pokemon games isn't to please the existing fanbase, but to provide a oppotunity to get children who were too young last time around to start playing.
It's all true, kinda like the new MLP cartoon you are not the game's demographic. The developers can add in little nudges here and there to acknowledge your existence, cause they just love your admiration for their hard work, but at the end of the day they are making a game aimed at school kids to whom things like easy to understand gameplay, flexible story, and the social aspect of trading is essential to the game.
Your argument about the Battle System.
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I would actually love to see a Pokemon game that had real time battles. One of my dream games would be a SSB style brawler with every single Pokemon a playable character. Their 4 moves could be mapped to the B button while the A button takes care of weaker variations of Bite, Tackle, Scratch, and so-forth. That being said though, the Pokemon games are about training your Pokemon to battle each other, not taking control over them and battling with them as avatars in some weird anime knockoff. Pokemon games are still one of my favorite Turn Based RPGs, and one of the few I can play without getting bored (The others included Golden Sun).
Also, turn based is a lot more suitable for a portable game. You can look away from the game for a moment without worry or having to pause during Turn Based Combat if you're out and about, need to catch a train, or someone yells "DUCK!"
Your Argument about the Story
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For reasons other then how it's told I'm not the biggest fan of Black and White's story, but so far it's had the deepest storyline of any of the main series and for what it was I did not mind it. I don't think adding anymore would help it, Pokemon's story has been simple enough with simple enough goals that any player can understand what they need to do and how to do it. Adding anything to it makes the game more about the characters and story then the gameplay, building your unique team, and the resulting interaction with other players.
Your Argument about the Multiple Versions
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Finally while I'd agree it is annoying to still run the whole two version gimmick it's understandable why they still do it. It was meant to make the Pokemon game more sociable, and to put it bluntly if you need to buy both copies of the game just to get all the Pokemon then you need some more Pokemon playing friends. Gamefreak can probably remedy this by adding a randomizing code into one version that restricts some Pokemon from being found in one cartridge and not the other, but I can see that annoying some people that have a system going with a friend where they each get different versions to help each other collect all the Pokemon. In short, selling 2 versions is the middle ground between forcing too much social interaction between players and not forcing enough. If you want to be able to finish the game on your own there are plenty of single player games out there for you, but Pokemon isn't one of them, it's primarily a multiplayer experience.
Your other Arguments
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Everything else you said, about evolution and leveling, I can tell you right off the bat that wouldn't be good for the series. Instant evolution is just lazy, if you really wanted to collect all the Pokemon in the game the least you can do is take on the challenge of training them. If not then you can just tell yourself "It's just a game, I don't really have to collect them all." The argument that it's too easy to power level with only three Pokemon makes me wonder how much of the game you understand. The concept of leveling in the Pokemon Titles is easy enough for a kid to comprehend and I'm sure there are Pokemon that can wipe out almost all opposition, but all it takes is one decent level type advantage to derail everything. That is one of those aspects at the core of the tried and true Pokemon gamplay.
And as for your last bit about not being able to catch fainted Pokemon, I agree it can be annoying but changing that would just make things far too easy. Especially with Legendaries.
My issues with the Pokemon Titles
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As for Problems I DO see with the Pokemon games, I can agree there are some and I've had my own ideas on the subject.
Story:
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For starters, while the stories have been good I feel they're drifting into the realm of over-the-top antics. To summarize, the first game was about a young boy who set out to train a team of Pokemon in order to collect badges and battle the greatest trainers of the region. Along the way he had several run-ins with Team Rocket, a Mafia-like group who's intentions were to gain power through the use of Pokemon, including experimenting on them and stealing Rare and Powerful Pokemon from other trainers. Using the trust and friendship between himself and his Pokemon, the boy put an end to Team Rocket's abuse of Pokemon and finished his quest to be the best.
Cut to Black and White, there the story is about a young boy who starts an adventure with two of his friends, all three with different goals. Cheren want's to be the strongest, Bianca just want inner strength, and you have the same goals as the boy from the first game. In your travels you watch as Cheren and Bianca learn valuable lessons about strength (an aspect I really enjoyed) and had several run-ins with a almost cultist party of Anti-Trainer activists run by an insane king who wants to rule the world by conditioning his heir to hate humans and assume the role of a prophesied Hero who's meant to change the world. Turns out then that you are the chosen Hero and you have a climactic battle with Legendary Dragons at the top of a Castle that rose from the ground.
If you get what I"m going for
(without even having to mention the Legendary battles involving the Earth, Sea, Air, Time, Space, Shadow Dimensions, and eventually the God of everything), it's that Pokemon has taken a leap from a story more rooted in Science Fiction with story aspects and a majority of Pokemon that have explainable, almost reality resembling qualities, to something so bizarre, over-the-top, and mythological. While I'm sure some prefer it this way, the reason a lot of people jeer the newer Pokemon designs are due to this over-the-top nature they've adopted over the years. It's made for some good games, but it's gone too far.
Gameplay
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The gameplay is solid, but one thing is for sure; after a certain point it becomes tedious and the challenge is lost without taking it to league matches. Gamefreak has done something in the past that I'd wish they'd expand upon and that's Re-Battles.
I find myself, most times, retraining a new team after the Elite 4. New Pokemon, Pokemon from other games of mine, that whole deal. Except the way they have it now this is very, very tedious and it results in nothing more then a grind until I'm of a level where I can refight the Elite 4 or any of the pre-determined re-battle opponents.
What I'd like to see though, are Re-Battlable Gym leaders and trainers with area based levels and teams that will change based on the Pokemon in your party. That way, you can basically replay the game with a new team anytime after the Elite 4. The story will be over, but at least the grind of wanting a new team will be eased and you can actually give yourself a challenge while training your new team beyond wandering into slightly higher level grass.
On a second note, I don't like the BP system. If anything, that's a little tedious
(Goes back to the it's too tedious to even waste my time on it.)
2 Pokemon = 1 Battle
7 Battles = 3 BP
16 BP= 1 Good Item
35.3 Battles = 1 Good Item
At least 8 Good Items to collect
282.4 Battles = 8 Good Items
Improvements I'd like to see in future Pokemon Titles
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Was going to call this part innovations, but innovations are rarely discussed prior to release as innovations by creative teams
(They refer to them as "Good Ideas").
Branching, Choice Driven Events.
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What better way to make an RPG game more about the player is to have choices that yield responsive results. From as small as getting different items for different answers
(Something they already do) to having that choice affect some else down the line resulting in a slightly different outcome for characters. Replayability is one thing, but it'd also make the player feel more in control of their character and influence more of what the next step is then just what Pokemon you used to get there.
There are Major plot points that, arguably, you shouldn't miss. IIt's hard to picture a game where you can completely ignore the Villainous team, but maybe a nice dynamic would be if you decide to ignore them and not meddle in their affairs they decide to come after you for your powerful Pokemon you've been training. Things like that can really add a bit of "What will happen next" and "did I influence this" to a game who's story has been pretty predictable up to this point.
Sub-Abilities
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This is nitpicky, but I wanted to add this. This mainly involves the ability "Levitate" and how I think it, and a few other abilities possibly, be added only as sub-abilities that a few Pokemon have.
For those unaware, Levitate is a special ability that makes your Pokemon immune to Ground Type attacks. It's normally given to Pokemon who, based on their sprite, do not come into contact with the ground or and hover above it
(as in the case of ghosts). These Pokemon look like then can, and should, be able to avoid attacks like Dig and Earthquake, yet without the ability they're sunk. This results in them only being able to have this ability and no others, which in a lot of strategies the choice of ability is a major factor in move set. Without multiple possible abilities, Pokemon like Flygon end up with very little quality move sets. Like I said, nitpicky.
Summery
To summarize, since I went into this post not expecting to write a whole article on the subject;
Your Arguments and my Retort:
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1.Turn Based vs. Real Time is a Personal Preference and Turn Based just happens to be more suitable for Portable Titles.
2. The story is simple enough to where it's more vital that you focus on your influence in the game rather then the NPC characters influence.
3. Multiple Versions foster Socializing in a more controlled manner then randomly selecting catchable Pokemon or making all Pokemon catchable.
4. Instant Leveling is Lazy, and if you're not motivated to try leveling then just repeat to yourself it's just a game you don't really need to.
5. Higher Levels don't always equal advantage in battle, though most times they do to offer a easier, fun experience to smaller children.
Problems I see with the games:
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1. The stories and Pokemon are getting way to Over-The-Top and should return to more grounded roots.
2. Previous trainers and gyms not able to be re-battled or only able to be rebattled with super powerful Pokemon..
3. The tedious BP system.
Things I'd like to see included:
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1. Choice influenced story elements.
2. Sub-Abilities are a small change that we can do without but would make my Flygon cooler.
Extra Note
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Is it just me, or is it weird that as soon as you beat the Elite 4 in Black and White, the strongest Trainers in the Unova Region, the next route has you battling trainers with Pokemon 20 levels above the Elite 4. So much for them being the strongest.