Wouldn't the original games be marked as non-canon because of the remakes?
Also, Maxie and Archie gave up their evil deeds after you stopped Kyogre and Groudon and become part of the good guys, and Cyrus is forever trapped in the distortion world with no way to escape to the real world (a fitting end for pretty much any villain who is that insane). Ghetsis, on the other hand, got away with everything because of the Shadow Triad, which caused speculations for BW3 (from BMGF that is). I've seen some people wanting him return, so he could get the proper punishment he deserved.
No Remakes would be Non-Canon/Alternate reality as they usually change some aspects to contradict
originals. Original versions are always Canon and trump any remakes seeing as they are the original story.
Archie and Maxie: They acknowledge that what they did was wrong and "Say" they are turning themselves in, but there is no proof that they do. Its just suspected that they went to jail. There is no proof that Cyrus was left in the Distortion World in Platinum, he also was not in the Distortion world in the original set of games so according to the originals for Gen 4, Cyrus is still at large. Ghetsis gave up when Kyurem was defeated and was forced to run away by the Shadow Triad after he himself lost.
A few quotes of Maxie and Archie when they release their Super Ancient Pokemon.
Archie in Ruby:
"Do you understand now, Maxie? Do you finally see how disastrous your dream turned out to be? We have to hurry! We have to do something before the situation goes completely out of control! <player>... We, Team Aqua, had been pursuing Team Magma to prevent this from happening. You've been very helpful, but I fear the worst has happened... It's gone too far for a child like you to manage... Leave things to us, and get out of here while you still can! This defies belief... A super-ancient Pokémon... Its power is unbelievable. It has upset the balance of nature..."
Plays the good guy role and tries to make Maxie see the error of his ways and goes off to try to stop what happened. Nothing is shown of his afterwards, though in Ruby Team Aqua were Anti-Heros as they were bad guys fighting to thwarts the evil deeds that threatened the balance already there through their own means which usually broke the law.
Archie in Sapphire:
"What happened... What is this wretched scene... Did I... make a horrible mistake? I... I only wanted..."
Emotional break down after seeing Kyogre lose control. Nothing after that.
Archie in Emerald:
"Kyogre and Groudon both flew off to who knows where. The weather in Hoenn has returned to its normal state... Haha... Hahaha... Maybe what we were trying to do was something small, even meaningless, to Pokémon..."
Realized that what he was doing seemed meaningless. Doesn't say that they'd stop or that they'd give up.
Maxie uses the same lines up to Emerald:
"So the super-ancient Pokémon weren't only Groudon and Kyogre... After all our frantic scheming and fruitless efforts, that one Pokémon's simple action puts everything right again as if nothing had happened... Fu... Fuhahaha..."
He's talking about how Rayquaza undid all their work.
Either way neither of them apparently turned themselves in like I thought. Maxie can still be found on Mt. Pyre and all he says is the players name. They disband like all evil teams do, but both are still at large.
Cyrus from Pearl/Diamond:
"What is truly ultimate to you? What do you consider perfection? The most important thing... What shines the brightest... Telling you is meaningless. But I will not give up. I will become a deity one day... And I will make the ultimate mine..."
He didn't give up and disappears with Mars and them. Still hell bent on creating his perfect world.
In Platinum:
"Silence! Enough of your blathering! That's how you justify spirit as something worthwhile?! That is merely humans hoping, deluding themselves that they are happy and safe! The emotions roiling inside me... Rage, hatred, frustration... These ugly emotions arise because of my own incomplete spirit! ...Enough. We will never see eye to eye. This, I promise you. I will break the secrets of the world. With that knowledge, I will create my own complete and perfect world. One day, you will awaken to a world of my creation. A world without spirit."
Again he continues with his attempt to recreate the world. Doesn't really say he was trapped in the distortion world, especially since he leaves the area before Cynthia comes back to take you home. Cyrus could have easily left before you or found another way out like the ruins where you find Giratina in D/P.
Giovanni's based on HG/SS shows that he had every intention of recreating Team Rocket. When the player foils him, he throws a fit of rage before leaving. While he may have gone off to train more, very little is said about what he planned for the future. He didn't take the defeat very well though. Similar to Ghetsis' rage at being beaten by children twice. The possibility of Cyrus, Ghetsis, and Giovanni still being obsessed with their respective teams is very high. Maxie and Archie, as stated before in the Remake thread, can find alternate reasons for starting their plans back up with more secure means of controlling the super ancient legends.
Since none of the leaders were effectively arrested, they are still free to roam around and build bigger and better plans for world conquest.
All of them were still left open with unanswered questions, and at the same time the effective stories were closed upon climax for each respective games.
Kinda wouldn't be too surprised in two of the hell bent ones make a return with the new bad guys in X and Y. Seems perfect for Ghetsis and Giovanni since both of them dealt in genetic manipulation of specific legendaries. Cyrus wouldn't fit as well, but there is always the chance that he can recreate a new world using the new legends. Though I personally doubt any of them will make a come back, the thought is still there.
Water/Electric Froakie..........Interesting, though he'll most undoubtedly lose the Benjamin look in his second stage. Still personally hope for Water/Flying.