Saint Seiya Omega/WMG

Kouga is Saori and Seiya's biological son.
Okay, I have to call this out since seems it obvious (or at least easy to speculate), Seiya and Saori indeed got intimate with each other, but since she is a Goddess and he is merely her Saint, such relationship can't be made public, so the couple made the pregnancy a secret (quite easy since only a few people can enter Athena's chamber); when the baby was born the rest of the Sanctuary was told that Kouga has been found in the Sanctuary's vicinity, and that Athena took a liking to him and wanted to raise him herself.
 * I'm gonna be more upset if Kouga is not Seiya's son. >:(

Shiryu is a Gold Saint, Libra Shiryu.
If he gave his Dragon Cloth to Ryuuhou, he must have been promoted to a Gold Saint, wearing the Cloth from his master that aided him as much as Sagittarius did for Seiya.
 * Likely Jossed. Shiryu has lost all five of his senses in an unspecified battle, and has taught his son everything he knows using his cosmo alone. It's still possible that Shiryu was an acting Gold Saint (and is now on a position similar to his master's, as a Gold Saint that can't really take action) during said battle, though.
 * Kinda hard to call this one out; since a Gold Saint must be of the same zodiac sign as the armor he intends to wear. Plus Shiryu is strong enough that he could at least wear the armor and move it using Cosmo; his whole schtick is being the guy who fights with a handycap after all. (and it would be amusing to see him ditching the Libra armor to fight at full power)

Kouga is Mars' son.
Admittedly, I originally came up with this theory simply because the entire "Saori and Seiya are Kouga's parents" thing is just so typical that it almost counts as an Un Twist. Keep in mind that Omega is a retooling of Saint Seiya for a new generation. Today's kids are better at guessing whats going to happen next and want plot twists deeper than that. Perhaps Athena rescued Kouga from Mars as a child for his saintly status, and that was what Revoked Mars' initial attack. And for less speculative in-universe evidence, Mars is shown to be distinctly interested when Kouga's element is revealed to be light. Maybe he knew that light was his son's element?
 * From what I've seen; Light is a very rare element to develop and it looks more like Mars was shocked that a Light user arose, since it very obviously opposes his dark power. Kouga being Seiya's son while cliched would be expected and welcomed. I'm more upset about the main characters not being the five man band; specially since there is a more likely Cygnus heir that wouldn't be somebody's son. (The little kid that used to watch Hyoga train. But since this show is seemingly based all around element battles and Ice would be a repeat of water well.. *sigh*)

This series is the Dying Dream of Seiya, after he is at the end of the Hades arc.
That would explain all strange things that happen in this series (such as Mars weird appearance and the changes of the cloths)
 * But Seiya was never  Even Lost Canvas explains that

Seiya is actually dead.
Following the series tradition of having the Sagittarius Saints being more spiritual guides.