[size=78%]To sum some ideas up briefly:[/size]
1. Shake up the structure - the series has used the same tired "8 Gyms + Elite Four + Champion" structure since the first game. Why not shake things up? Why not have an actual narrative taking the player through the game world rather than this checklist-style "field/dungeon -> gym -> field/dungeon -> town-field/dungeon" structure we have right now? For that matter, does EVERY game have to be based on the concept of you being this "child from a small town who sets out to capture all the Pokemon, racing against your rival"?
2. Drop the random encounters - I despise random encounters. They're a technical crutch used in the early days of gaming because the hardware couldn't handle having the enemies on-screen. That was understandable for its time, but it's 2013 now. I'm sick of being ambushed by Wild Zubats on my way to trying to get somewhere else. Let me spend my time pursuing & capturing Pokemon, rather than running around in tall grass for hours on the off-chance the Pokemon I want will appear.
3. Modernize the combat system - It's 2013. I'm not entirely against the series remaining turn-based (although I think something like Square's old ATB system would work well here), but I'd like to see a greater range of strategic possibilities and a more active element, especially when it comes to environment and character interaction. For instance, if I'm in combat where I have 2 Pokemon out against a Pokemon that is super-effective against one of my Pokemon, and one of my Pokemon's a flying type. How about letting me have my flyer pick up my other Pokemon and keep it out of harm's range of the attack that would have wiped it out? Maybe there's a cliff in the environment where I can strategically position my Pokemon for additional range and higher evasion, making it harder to take out. On the other hand, maybe being on that precarious cliff is a bad idea, because my opponent could fling an attack at the cliff itself to collapse it and deal massive damage to anything currently on it?
And while we're at it, let's speed the battle system up considerably. There is so much needless B.S. text in every Pokemon game that you have to constantly either sit or page through that it probably comprises at least half the game's running time.
4. Make a real Pokemon multiplayer console RPG - No, I'm not saying to make a Pokemon MMO. However much that makes sense, that's just not the kind of game Nintendo is good at making. No, I'm instead suggesting a large-scale open world Monster Hunter-style console RPG that players can play either singleplayer or multiplayer both online and offline. And while we're at it, ditch the rigid overhead grid-like world Pokemon's used since the first game. Let me explore this world. Players can join your game at any time with their own Pokemon, with the ability to capture and trade with you while in your game. Any Pokemon they capture goes back with them. Just imagine epic 4v1 battles against the Legendaries with your friends in a big open environment, rather than the usual "I'll just hit this thing into near-death & then paralyze/put it to sleep long enough to hit it with an Ultra Ball" strategy.
Those are some ideas that come to mind right now.
First and foremost, thank you for taking the time to reply to my post, Broodwars. I would like to go point for point on these suggestions, because I do like some of these!
1. Pokemon Colosseum and Pokemon XD actually dared to do that, and got looked down upon for not being 'full' pokemon adventures. I'm not saying this is a bad suggestion, I'm saying that it's probably a choice Nintendo and the Pokemon Company feel is damaging to the series. I do suppose being a kid just starting on their journey is meant to hit a target demographic and gives them excuse to litter the landscape with the usual tutorial NPCs. 8 gyms is probably something their playtesters feel is the proper span of game length that is easy to measure... again, it comes from fear of burning out players by not having the usual metric of progress. They have tried interesting angles with the evil crime syndicate in Black/White and are trying something new with the whole Rival thing in X/Y so far, so... That's something, I guess?
2. REPEL IS YOUR FRIEND. No, seriously. I can live with the random encounters because there are methods of mitigating and controlling the ebb and flow of them. There's so many things to take into consideration by dropping random encounters like how will pokemon respawn? will finding rare pokemon require repeatedly leaving and reentering the room they have a chance to spawn in? how hard will it be to evade fast little bastards like Zubats from just swarming you over and over again and adding to your frustration? If anything, not knowing is a bit of a surprise that I personally enjoy, but I understand that it's not really for everybody! Still, this sort of take cues from Monster Hunter thing you suggest later could be potentially interesting for adding overworld behaviors to Pokemon and adding ways to bait out certain pokemon and interact with them on the overworld could be great.
3. They've actually been adding in more support oriented abilities and attacks for the past few gens to try and layer on strategy. they've severely trimmed down on the text and things like weather no longer have in-between turn animation as of Gen 5. terrain changing moves, moves to give temporary immunity or weaknesses, and supporting attacks have been a big part of a push to make Double and Triple battle a more robust experience. Doubles and Triples end up being such rare experiences in the main game and doing it proper in any competitive sense usually means building a separate team focused on double and triple battle synergy. Like I said in my original post, I don't know about adding some sort of real time or even ATB elements. Pokemon's multiplayer at it's core is cerebral Rock-paper-scissors where if you're playing an opponent who has the same level of mastery as you do, are constantly trying to bait and switch into each other's traps, and I don't think that gets retained if you and your opponent's actions don't play out at the same time. I don't even know how one would go about upheaving the gentle balance that the 4 move mechanic holds for things without upsetting a lot of fans. I do like the idea of attack range and such and the mystery dungeon games fiddle with that... then again, the mystery dungeon games are awful Chunsoft dreck.
4. Without the real time elements you mentioned before added in, I don't really see how doing this sort of instanced multiplayer would be fun without being bogged down in having to meet JRPG standards of visual spectacle, which also usually means good chunks of attack animation splitting up each player's turns. If anything now we're veering off into Pokemon Rumble territory, which is yet another spinoff nobody I know really even cares about.