Okay, here are ALL of my thoughts about the Pokemon franchise:
Ahem...
I really love playing Pokemon and I love how it has evolved since Red/Blue version. The part with all of the new Pokemon, which totals up to 450 something, it should just end right there, no more new Pokemon. The last Pokemon, Arceus, the Pokedex says that it's "The God of all Pokemon." So, I mean, where are you gonna go from there? Seriously, no more new Pokemon, we have enough, thank you.
The plot:
Yeah, they should come out with a new kind of pokemon game with a more involved storyline that is darker than what it is right now. I really thought that they had it going when they came out with Pokemon Colosseum and XD. It was fun, dark, the bad guys were... slightly more sinister and evil than the gay bumbling team rocket or galactic. I once read a fanfiction that made team Galactic look like the most evil, badass bastards to ever roam the country. Thse guys had Bombs, guns, were freaking criminal masterminds, and it took an entire police force, army, and military to SURVIVE ONE ATTACK against a town, instead of all of them being taken out by a single KID. And when I actually saw what they actually are like in the game I was like

what the heck? These guys suck! So, yeah, better villains with a better storyline. And make sure that everybody that you meet isn't completely stupid or not right in the head to some degree, because that really gets annoying. I hate how the plot is focusing on little kids when older teens are playing this too. They risk alienating most of their gamers by doing this. It is possible to make a story that's fun for little kids, yet dark enough for adults.
Gameplay:
I really liked out4blood4's gameplay ideas, those should be incorporated into the game as well. The online MMO is really interesting too, but I wouldn't care if it wasn't in there. Customizable characters need to be in there too. Pokemon Revolution tried this attempt and it kinda' flopped, if it had been better then I would've suggested that. No more HMs because that gets really really annoying that you have to keep switching to your HM slave. And you also can't delete the HMs unless you find the freaking Move Deleter, which just makes it really really inconvenient.
NO MORE EVENT POKEMON!!!
Dear God! This one ticks me off the most. They have an event, like in Florida where if you live somewhere far away from that place, you'd have to charter a plane in order to get there, which your whole trip is going to total a whopping $1500 or more JUST FOR A PIECE OF DATA. It is seriously not worth that, it is so much easier (and cheaper) to buy an Action Replay and use that to get them, which makes your feel like a big cheater in the long run. Stop with the event Pokemon, it's annoying, and stupid. If you're gonna make the legendary Pokemon, then have it so that it is actually possible to get them in the game instead of going to these stupid events.
To put more emphasis on what would make a good game, I think that they should go back to making something like Colosseum and XD. I really liked it. It was new, interesting, and it put a whole new perspective about what the Pokemon world could evolve into and what it can easily become, not just "I'm gonna become the greatest Pokemon Master EVAAAAR! Gotta Catch 'Em All!" Put a new direction into Pokemon and it could be the greatest game in Pokemon ever.
I think that's all I have on my mind about Pokemon.