I don't see them releasing a YO4 to coincide with Zexal. Mainlyb because they haven't even finished the full running of YO3 after almost a year now e.g map buttons. However, it's probably editable to the point that they could change the title screen to a different picture with all the main characters instead of Yusei for instance.
...On the other hand YO3 itself is kind of based on Neo Domino City from the anime so if the new show is set somewhere else then it would be weird. Honestly though, I've read the first manga chapter of Zexal and it doesn't seem great, I'm sure it will be another GX monstrosity aimed at younger viewers
Spirit- Dark Magician (blue armour)
Signature Decks- Darkest Magic. Spellbound. Dark Sky. Wildfire.