Holy shit, about time we have an actual thread on here. I'm glad to see others here also enjoy the newest YGO franchise installment.
For anyone who is behind, it is true that the Fortune Cup drags a bit (even if I did personally like Rua and Ruka's battles), but the series really picks up at episode 25. I highly suggest you catch up. There is a little annoying filler in season 3, but overall the latest episodes have been very good.
Here's a bit of info on the villains in season 2 and 3 for anyone curious about what to expect:
The Dark Signers, the group that has been battling the Signers for centuries, makes a comeback and puts their plan into motion. They plan to offer Satellite as a sacrifice in order to resurrect the King of the Underworld. While cliche, the Dark Signers themselves are all very interesting and the battles are overall great. Even the worst battle, the battle with Rua/Ruka, still has its high points. All the Dark Signers wield the evil dieities sealed in the Nazca lines, the Earthbound Gods. And yes, they are all based off the actual Nazca lines.
Here's some info on the Dark Signers themselves:
Kiryu - He is a childhood friend of Yusei, Jack and Crow (Crow is introduced in season 2, for those who haven't seen him yet.) They formed "Team Satisfaction" back in the day, and planned to turn the scum of Satelite into a better place by wiping out all the Dueling Gangs (well its YGO, so Dueling is always going to be a part of it, whether or not it makes any sense.). Eventually though, Kiryu becomes obsessed, to the point where he begins trying to take on Security as well. This leads to him killing a Security officer, and Kiryu is mislead into thinking that he was betrayed by Yusei.
In present time, Kiryu has become a Dark Signer, after Rudger approached him and helped him escape from jail. He seeks revenge on Yusei, trying to kill him, and he almost succeeds. So Yusei's character arc for a good portion of this season is to bring his former friend back to his senses.
Carly - She starts out as a random media maniac looking for the latest info on Yusei, who won the Fortune Cup. She ends up falling in love with Jack, but is killed by Divine (the leader of Arcadia Movement), who uses his Pyshic Dueling powers to blast her out the window of a skyscraper onto the pavement below. Immediately upon dying, Rudger turns her into a Dark Signer. Now she is forced into conflict with Jack. So Jack's character arc in this season focuses on his conflict to save Carly.
Demak - This guy is the least interesting of them all. He has hardly any backstory. His reason for existing is that he stole Ruka's Ancient Fairy Dragon, and Rua ends up Dueling him while Ruka battles the "Monkey King" in the Spirit World, which is using Demak's power to destroy the Spirit World and turning all Duel Monsters Spirits evil. The mini plot here is pretty meh overall, but at the very least, the twins get a chance to shine for a change. Ruka's character arc this season is to get back Ancient Fairy Dragon, and Rua's is pretty much to help his sister out.
Misty - She believes that Aki was the one responsible for killing her little brother, so she has sworn revenge on her. Misty became a Dark Signer after committing suicide (she ran her car off the highway in a depressed state.) Aki's character arc, aside from her transition from her lonely, socially inept self, is to settle the score with Misty and find out what really happened.
Bomber - After being arrested in Fortune Cup after trying to kill Godwin, Rudger confronts him and feeds him some bullshit about using the power of the Dark Signers to avenge his little brother and sister, who were consumed by the Earthbound Gods. Rudger pretty much kills him by sticking him inside the portal to the dead, and Bomber ends up snapping, battling against Crow.
Rudger - The leader of the Dark Signers. He is also the brother of Godwin. His past story coincides with Yusei's father. Rudger was manipulated by Yliaster into screwing up the Momentum and causing Zero Reverse, that took out a 1/3 of Neo Domino City 17 years prior. He also became a Dark Signer at this time. He was the fifth Signer before this happened, but he cut off his own arm in order to protectthe Signer power, and entrusted the arm to Godwin.
Rex Godwin - While maintaining a sort of anti-hero status throughout season one and almost all of season two, Godwin reveals that his true goal was to become "God" by obtaining the power of both the Dark Signers and the Signers. He allowed himself to lose his Duel to Rudger so he would be killed, and then revived as a Dark Signer. He then attached Rudger's arm to his own, mixing the powers of the Signers and Dark Signers. He is the final villain of the second season, and faces Yusei, Jack and Crow in a Battle Royale Riding Duel.
Season 3: While a mixed bag overall, season 3 has two focuses. The first is Yliaster, a group that has had an influence on all the major changes in the history of the world. They are first mentioned in season one, and were revealed to be pulling the strings behind the Dark Signers and Godwin. The Emperors of Yliaster, Placido, Luciano and Jose, are three mysterious men that were chosen by the gods. They wield the Machine Emperors, which hold the power to seal Synchro Summons. The second focus is the World Riding Grand Prix, a Duel tournament the gang enters. Yliaster are pulling the strings behind these events.
In recent episodes, the Emperors of Yliaster are revealed as strange cyborg men. Their bodies are machine. They possess super human strength and wield strange weapons and powers. Yusei and co are seeking stronger powers in order to be able to fight them.
Currently, Jack is paying a visit to the Nazca plains, where the strongest Earthbound God, the Crimson Devil, is testing his strength.