1. The story will take place at the same time as sun and moon but in another paralel Universe, in which Mohn (confirmed to be Lusamine's husband and Lillie and Gladion's father) never disappeared and now he's the president of the Aether Foundation. Lusamine is not bad anymore, and Lillie and Gladion have a normal life. In fact, Lillie is a trainer and she's your rival. Gladion works as a researcher in the Foundation with his Type: Null and later will travel through Alola and train to become a strong trainer. He'll help you a lot through your trip.
2. The Aether Foundation is not the evil, and Team Skull is not a criminal gang, but a group of people that work to stop crime in Alola with their boss Nanu. Guzma isn't part of Team Skull, but he's a member of the Elite Four in Ultra Sun. (Plumeria instead of Guzma in Ultra Moon).
3. Faba is so upset that he's not the president of the Aether Foundation, so he creates his own Organization, the Z-Corporation, settled close to Tapu Village, and Colress is his Admin. Their purpose is to use the power of Z-Power to travel to the Ultra Space and catch the UBs to invade Alola and rule the world.
4. Mohn and Lusamine will give you the Cosmog they had been protecting in order to stop Faba, but the Power of Solgaleo/Lunala won't be able to fight the UBs, so they'll give you a Master ball to catch Necrozma in Tencarat Hill and then Lusamine will give you the U-Core, which allows to fuse Solgaleo/Lunala with Necrozma and then fight the UBs (in the Islands) and Faba (in Ultra Space, he has a new UB with no typing which looks like an enormous Hydra).
5. Zygarde 100% will fight against Guzzlord (cutscene) and the Tapus will fuse in order to create a huge Totem Pokemon to fight the UBs.