I went through the wiki and this is all I found up to around the 6th gym
Ancient Ruins: Steelixite (Fire) Inside, room L3 (requires Tesseract) (route 2)
Suntouched city Great Ball :Cloud level; in front of the wall with music notes (requires Tesseract)
Zapdos can be encountered on the cloud level to the east of the Suntouched Gym if the player has the ability to use Tesseract and Relic Song.
Route 3 Sceptite In the grass section at the west of the road (requires Tesseract)
Vipik City Beedrillite Directly west of where Damian was being held hostage (requires Tesseract) (vipikDump)
Route 5 Sudowoodite Near the northeasternmost entrance to Samsara Cave (requires Waterfall and Tesseract)
Samsara Cave Delta Pidgeotite 1F, south entrance; In the middle of the Delta Pidgeot Shrine (require Surf and Tesseract)
Route 6 TM117 Dragonify Northwest of the entrance to Roggan Town, after obtaining Tesseract
Heilos City Sablenite Starting from the Black Market: Down, all the way to the right until colliding with a wall, southwest in this new room, and then to the right (requires Shaymin DNA and Tesseract) (sewers)
Salamencite Found at the top of the tower (requires Tesseract) (jade Tower)
Utira Town Gengarite Located in the second room of the Abandoned Wing (requires Tesseract) (Libary)
Route 8 Audinite Directly East of the northernmost house (requires Tesseract)
Miara Town Milotite On the left part of the island (requires Tesseract) (lush Island)
Delta Galladite Inside, B2F; left from where the player fights Audrey (requires Tesseract) (Whirl Island)
Delta Gardevoirite Inside, B2F; right from where the player fights Audrey (requires Tesseract) (Whirl Island)
Maelstrom 9 Sharpedonite B1F, room 10; in the middle right corner (requires Tesseract and the phone call from Damian) (abyssal Base)
Kepler City Metagrossite Located where the player fought Anastasia (requires Tesseract) (kepler Gym)
Nasca Town Heracronite In the Apricorn fields in the western part of town (requires Tesseract)
Delta Bisharpite Southeast of where the player finds Delta Pawniard (requires Tesseract) (power Farm)
Hekate Town Delta Froslassite 1F Room 3; to the right of the Delta Snorunt (requires Tesseract) (Fiery Cavern)
Delta Glalitite 1F Room 3; to the left of the Delta Snorunt (requires Tesseract) (Firey Cavern)
Selene City Gothitite Use Tesseract in Diana’s room(Selene Gym)
Mysterious Hideaway(need it for the Ancient Tower)
Dragon Ruins Delta Bergmite can be encountered east of the ritual altar after obtaining the ability to use Tesseract
Route 14 X Attack Below the right side of the train tracks (requires Tesseract)
Hyper Potion (requires Heart Swap and Tesseract)
Garchompite (requires Heart Swap and Tesseract)
Crystal Cave Timer Ball ×3 Area 2; in the 3 rocks on the top right after using Tesseract for the 2nd time (hidden)
Full Restore x1 Area 2; at the top of the room in between some rocks (requires Tesseract)