The biggest connection between Kanto and Hoenn is the events that took place in the Sevii islands. In Pokemon Firered/LeafGreen and Emerald you can go to the Sevii Islands and catch both Lugia and Ho-oh in the Navel Rock and Deoxys in the Birth Island. After both the Kanto and Hoenn protagonist becomes the champion of their region, the new Hoenn champion goes to the Battle Frontier to challenge other strong trainers while the new Kanto champion goes back to the Sevii Islands to stop the remaining Team Rocket members. After Team Rocket gets defeated one of the remaining Team Rocket members says that he will try to find Giovanni and rebuild Team Rocket which becomes the main goal three years later in Johto. With all the Team Rocket members gone Red gives up his position as the champion and goes to Mt.Silver to train day and night. Some time after the event between Kanto and Hoenn, Blaine (the seventh gym leader in Kanto) moves his gym to the Seafoam island because of the Volcano eruption in Cinnabar island. With Giovanni now gone Blue becomes the eight gym leader and Lance is left in charge as the Pokemon League Champion.
Three years after the events in Kanto and Hoenn the Johto protagonist begins his/hers pokemon journey battling trainers and collecting badges until the hero comes across Team Rocket and discovers their true plan. A few members of the old Team Rocket are trying to reestablish the old organization and to do that they need money. For the past three years Team Rocket developed a machine that forced Pokemon to evolve. They finally completed the machine which they used in the Lake of Rage on the Magikarps who lived there so they were forced to evolve into Gyarados. Team rocket could then capture the powerful Gyarados and sell them for a high price. Their plans did backfire since a Magikarp who evolved into Gyarados was mad and started to attack everything around it. The Johto hero eventually founds the angry red Gyarados and stops it by either catch or defeat it.
The discovery of a red Gyarados where all over the news and this is the same news broadcast as the Sinnoh protagonist sees in Twinleaf Town before starting his or hers journey. Evidence on being the same red Gyarados from Johto is the cameraman who blocks the Entrance to Lake Valor in Sinnoh. The cameraman mentions that it was he who filmed the red Gyarados at Lake of Rage in Johto. An another link between Sinnoh and Johto is Jasmine, in HeartGold and SoulSilver you can see that Erika and Jasmine has a conversation and Jasmine mentions that she's going to enter the Pokemon contest in Sinnoh. So it means that after the Johto protagonist defeats the Elite Four, that is when Jasmine travels to Sinnoh so she can compete in the contest. In Sunyshore City the Sinnoh protagonist encounters Jasmine and in Hearthome City in the Pokemon contest and then competes against the player with her Steelix named Rusty. When she goes back to Johto, Jasmine offers to train the same Steelix and thats when the Johto protagonist has defeated all of the Kanto gym leaders. After the Johto hero stops the remaining Team Rocket members the hero goes to Mt.Silver to have one final battle against Red meanwhile somewhere in the Sinnoh region, the Sinnoh protagonist fights against Team Galactic and goes to challenge the Elite Four. After the Sinnoh hero defeats the Elite Four and Cynthia the hero becomes the new Sinnoh Champion.
In HeartGold and SoulSilver, the Team Rocket Grunt who stole the machine part from the Power Plant in Kanto returns to his home country the Unova region. He tried to reestablish Team Rocket but gave up on his plans when he got married. Now because he has a son when you meet in the Icirius City this means that the events in Unova takes place a few years after the events in Johto and Sinnoh.
An another link between generation 4 and generation 5 is Cynthia. After the hero in Black and White defeats Cynthia for the first time she will mention that the player character reminds her of the hero who faced Giratina back in Sinnoh.
In Black and White the hero travels through the Unova region while collecting badges and stopping Team Plasma but before the hero can face the Unova champion the hero must defeat the leaders of Team Plasma. With the help of the legendary dragon the hero stops Team Plasma and returns to the Pokemon League to challenge and defeat the champion. After the hero becomes the champion the hero leaves the Unova region to look for N. After the events of Black and White, Iris takes the position as the new Unova champion and waits for new challengers. Two years later the event of Black 2 and White 2 takes place where a new hero is introduced. The new hero must stop the broken Team Plasma and face the Shadow Trio. After stopping the bad guys the new hero will challenge Iris and becomes the champion of the region. The new hero who is now the new champion goes and finds N for an one last battle before ending the Pokemon journey.
Link to the one who thought and made a video of this:
