*EDIT* Please read my other posts on this thread before presenting your arguments. *END*
1. The stories of Pokemon games need to be better, not necessarily more mature, but need to be more immersive and detailed. There needs to be plot holes to be answered in other installments, there needs to be plot twists, surprises, revelations. In other words, Pokemon games need all the building blocks of a great story, and Pokemon games rarely have ANY of these things.
This article is a good example of something they are refusing to do that if they did would greatly help breathe life into this stale francise:
http://www.escapistmagazine.com/news/view/109149-Game-Freak-Wont-Let-Pokemon-Players-Be-Bad
There's no problems with not letting you be 'bad' so much as there needs to be a deeper story, would you want to be 'bad' but the gameplay to essentially be unaltered? What they need to do is focus more on the story and bring in some actual writers, they've said in the past that plot isn't given the best priority.
2. The overall plot of Pokemon games needs to change, with the exception of 2, (Colosseum and Pokemon XD: Gale of Darkness)ever since the first generation the goal of each Pokemon game has been exactly the same, go to a town, beat the Gym Leader, get a badge, go to the next town, rinse and repeat, while encountering an evil organization that isn't really evil or menacing at all that you take out, beat the Elite Four or whatever they're called that generation, become the Pokemon champion. Your mileage may vary, but this formula was done to death a LOOOOONG time ago.
It doesn't help that those games got mediocre scores or didn't sell well either, it makes them reluctant to try something like that again. They are probably in the "Don't fix what isn't broke" mindset, instead of adding something potentially risky they upgrade what we currently have.
3. This is something 1&2 would help with, people like me (I'm 24 BTW) that grew up with Pokemon are being completely ignored, no attempts are being made to keep us hooked. They never need to change anything because they market to little kids. This is for the same reason children's stories have been around for centuries without a change, it's because for every one person that grows out of it, there are countless more children that are growing INTO it. They need to find a way to serve all ages, not just kids.
One issue with trying to do this is most kids have very similar interests at an early age and very different interests at a later age that's harder to appeal to. It requires them to be able to keep the audience of people that have vastly different interests compared to a younger audience. What needs to be done is to make it more of a true 'Everyone' game instead of E meaning children. They need to drop silly things like bagon learning how to fly because it REALLY wants to.
4. The mechanics of Pokemon battles need to change, at least in the main game where the Pokemon's levels don't have to match, as long as your Pokemon CAN damage their opponents, all they have to do is power-level to beat anyone easily. This results (and I'm guilty of it too) in people just using one,two, or three (depending on if there are double/triple battles or not)Pokemon in every battle throughout the entire game, because it is a LOT less tedious than leveling up 6 Pokemon at once. The rest of your roster is just there to get you through obstacles. Also, all Pokemon in your roster should recieve XP for just being there, not just the ones that have been out, and it would be the full XP, as if they had been the only Pokemon out, and modifed by level so the lower level ones can catch up to the higher level ones.
They've been trying that with the black/white versions, overleveled pokemon's levels start to gradually plateu due to getting less and less EXP whilst pokemon that are lower level then the opponent get huge amounts of EXP. In Red/Blue there was in fact an item called an "EXP All" which did just that by the way, it never made a return.
5. Pokemon battles especially against the computer need to become much more engaging and not repetitive. They need to finally remove the turn based combat, which only required the player to know how to press the A button repeatedly, and change it to a action RPG, like Kingdom hearts or the Tales series, which even during really easy fights require you to pay attention.
They need to have more variation between sprites of the same trainer type, they need to feel like you're fighting different people. When you enter a double battle with two trainers of mirrored sprites, that totally destroys the effect. The turn based combat is quite fine, and there's no way theys make such a risky buisness move by changing up the combat. Pretty much ANYONE can play turn based combat, but not everyone can play action combat. This suggestion might be good for a spin-off game as a proof of concept, but not much beyond that.
6. Capturing of Pokemon should NOT be insanely tedious, the biggest problem here being that for no reason whatsoever Pokemon that faint cannot be captured, despite the fact that it would be much easier to do that way and that it happens in the Anime. Also, I know that rare Pokemon should be in there, but does that mean that I have to take out 100 small fry JUST to find that one Pokemon?!? Simple fix here, just have a system which would cause the odds of finding a rare Pokemon in an particular area to increase the more common ones you took out, eventually becoming all but certain.
The pokemon from XD and Colosseum were quite fun to try and catch due to the different mechanics. Namely you were catching other trainer's pokemon, and that due to that they were a threat and could actually KO you. What the main games lack is that after a while you get a high level pokemon with false swipe that just makes catching pokemon trivial. There needs to be more to catching pokemon.
7. Unless it's an extremely rare or story event Pokemon, you should be able to choose ANY Pokemon from that game's roster as your starter. I can't tell you how annoying it is to want a particular Pokemon at the start, but not be able to get it until almost the end of the game.
This might be interesting if implimented as a 'New Game Plus' where you restart the game from the start (All money, mons, and stuff are saved over) and you could be able to pick any pokemon you own as your starter.
8. Evolution should be forcable to ALL Pokemon, as well as via level, so that people that just want to evolve a Pokemon could just do so without having to spend hours leveling it up, and if they were actually going to use it, they would be rewarded with much higher overall stats.
There's a reason why some pokemon require trading, that's to facilitate communications between the player base.
9. Finally, one of the most important, stop releasing 2 games and eventually a third every generation. It wouldn't have to be easy to do, but there should only be 1 version where all the Pokemon from that generation could be caught in one game. The reasons for this are simple, many gamers may NOT have many friends which actually play Pokemon games, because trading is a long and completely unnecessary process that, if you don't have somebody else to link up with, you'll be forced to purchase 3 versions of the game, another of whatever handheld it is on, and a link cable, and most people that play these games and their families are NOT made of money. Linking should be solely for Pokemon battles between players and nothing else
As with the above it looks like a lazy cash in but the designers at game freak never intended for fans to buy all the versions. They expect them to trade for what they want from other people instead of just getting multiple copies. There's also online trading too you could try and use that.