Spoiler Alert!!! 

As far as Chapter 650

Main Team (Switch Team)

¤ Beedrill (M) (Sniper) (quasi-Elite) Obtained from the beginning of the story, While still Weedle, he had eaten the Zapdos's feather during the Tom Ritchie incident.

¤ Alakazam (M) (Magic Guard) (quasi-Elite) Obtained from kadabra research results of Gen Mew Team Rocket who managed to escape with eggs, in the forest near Saffron City.

¤ Togekiss (F) (Serene Grace) (quasi-Elite) Obtained when exploring the ruins with Steven and Shirona in the forest near Saffron City

¤ Aegislash (M) (Stance Change) (quasi-Elite) Obtained at auction from Phoebe, a future Hoenn Region Ghost-Type Elite.

¤ Monferno (M) (Blaze) (elite) Found in Groudon's space, has consumed Primal Groudon's carapace shard.

¤ Latios (M) (Levitate) (elite) Obtained from an egg after saving one of the "Draconid Tribe"

¤ Eevee (F) (Anticipation) (Senior) Obtained from Alliance assistance for Research.

¤ Dragapult (F) (I Forgot?) (Elite) Obtained in the Regigigas's Space, Dragapult is the result of an Ancient One's experiment that still survives because of her Ghost Type, having made a deal with Natsu to defeat her and make her to his Pokemon.

Hunter Team (Space Team)

¤ Snorlax (M) (Thick Fat) (quasi-Elite) Found in a cave blocked by a group of Wormadam in a cave not far from Solaceon City. 

¤ Bewear (M) (Fluffy) (quasi-Elite) Obtained while carrying out a mission for the Hunter's Guild from Team Rocket on an unnamed island.

¤ Oranguru (M) (Inner Focus) (quasi-Elite) Obtained on Mount Hokulani, Alola Region, while fighting for the Hunter's Guild seat 

¤ Audino (F) (Healer) (quasi-Elite) Obtained in Rayquaza's space, to become a doctor.

¤ Steelix (M) (Rock Head) (quasi-Elite) Obtained in Rayquaza space, suitable for pokemon hunting and research.

¤ Hatterene (F) (Magic Bounce) (quasi-Elite) Obtained in Rayquaza's space, after attacking Togekiss, fills the special attacker for the empty "Team Space"

¤ Hydreigon (M) (Levitate) (Elite) Found in the Rayquaza' space, one of the lords in the Rayquaza' space, was defeated after being beaten by a mob.

Pokemon on the Farm

Captured in the Regigigas' Space

¤ Tyrantrum

¤ Yanmega

¤ Cherrim 

¤ Cherubi 

¤ Etc.

Captured on Mission in Unnamed Island

¤ Milotic 

¤ Feebas 

¤ Etc.

Captured in the Alola Region

¤ Ninetales 

¤ Vulpix 

¤ Exeggutor

¤ Etc.

Captured in Groudon's Space

¤ Salazzle

¤ Selling

¤ Turtunator

¤ Noivern 

¤ Noibat

¤ Etc.

Captured in Rayquaza's space

¤ Shinotic 

¤ Morelull

¤ Etc.