Missing Mega Evolutions in Shuffle

Released thus far:

1. Mega Charizard Y
2. Mega Heracross
3. Mega Sharpedo
4. Mega Blaziken
5. Mega Absol
6. Mega Manectric
7. Mega Garchomp
8. Mega Latias
9. Mega Latios
10. Mega Gardevoir
11. Mega Steelix
12. Mega Medicham
13. Mega Swampert
14. Mega Charizard X
15. Mega Mewtwo X
16. Mega Abomasnow
17. Mega Metagross

Mega Evolutions of known Pokémon:

1. Mega Charizard X
2. Mega Pidgeot
3. Mega Scizor
4. Mega Mewtwo X
5. Mega Pinsir
6. Primal Groudon
7. Primal Kyogre
8. Mega Rayquaza
9. Mega Tyranitar
10. Mega Sceptile
11. Mega Swampert
12. Mega Camerupt
13. Mega Salamence
14. Mega Gyarados
15. Mega Diancie
16. Mega Gallade
17. Mega Beedrill
18. Mega Alakazam
19. Mega Aggron
20. Mega Houndoom
21. Mega Abomasnow
22. Mega Steelix
23. Mega Medicham

Unknown Pokémon with Mega Evolutions:

1. Mega Houndoom
2. Mega Gardevoir
3. Mega Latios

Edit(07.09.2015): Current pre-paid cards showcase Mega Sceptile and Mega Swampert, but they have not been released.
Edit(28.09.2015): Removed Mega Latias and Mega Charizard Y. Updated the Unknown Pokémon with newly released stuff.
Edit(05.10.2015): Removed Mega Absol.
Edit(02.11.2015): Removed Mega Gardevoir.
Edit(01.12.2015): Removed Mega Steelix, Mega Medicham and Mega Latios. Moved Gallade to known Pokémon.
Edit(28.12.2015): Moved Camerupt to known Pokémon.
Edit(05.12.2015): Removed Mega Swampert.
Edit(20.01.2015): Moved Aggron and Abomasnow to known Pokémon.
Edit(09.02.2016): Removed Mega Abomasnow.
Edit(16.02.2016): Removed Mega Mewtwo X. Added Beedrill and Alakazam to known Pokémon.
Edit(23.02.2016): Removed Mega Charizard X. Added Gyarados to known Pokémon.
Edit(15.03.2016): Added Houndoom to known Pokémon.
Edit(05.04.2016): Removed Mega Sceptile.
Edit(26.04.2016): Removed Mega Scizor, Mega Diancie and Mega Rayquaza.
Edit(28.06.2016): Removed Mega Gyarados.
Edit(02.08.2016): Removed Mega Steelix.
Edit(13.09.2016): Removed Mega Alakazam.
Edit (28.09.2016): Removed Mega Beedrill.
Edit (11.10.2016): Removed Mega Pidgeot.
Edit (01.11.2016): Removed Mega Metagross.
Edit(22.11.2016): Removed Mega Camerupt and Tyranitar.
Edit (21.12.2016): Removed Mega Salamence.
Edit(17.01.2016): Removed Mega Houndoom.
Edit(14.02.2016): Removed Mega Aggron.
Edit(13.06.2016): Removed Mega Gallade.
Edit(13.02.2018): Removed Primals. And condensed the list.
Edit(08.05.2018): Removed Mega Pinsir. All Megas are now available.

Remaining Stuff to be released in Generation VI

Unavailable Event Pokémon:

1. Phione
2. Manaphy
3. Meloetta
4. Genesect
5. Volcanion (announced)

Not released Globally:

1. Jirachi(Shiny)
2. Darkrai(outside of UK and Japan)
3. Shaymin
4. Victini
5. Keldeo
6. Arceus
7. Xerneas (Shiny)
8. Yveltal (Shiny)
9. Diancie (Shiny)

Not released outside of Movie events:

1. Non-Shiny Diancie(for Japan)
2. Arceus
3. Hoopa(for Japan)

Unavailable Items:

1. Elemental Gems

Not released outside of Movie events: N/A

Unavailable Alternate Formes:

1. Eternal Flower Floette

Unavailable Hidden Abilities:

1. Kangaskhan
2. Omanyte.
3. Omastar.
4. Kabuto.
5. Kabutops.
6. Aerodactyl.
7. Snorlax.
8. Sentret.
9. Furret.
10. Entei
11. Raikou
12. Suicune
13. Lugia
14. Ho-oh
15. Treecko
16. Grovyle
17. Sceptile
18. Mudkip
19. Marshtomp
20. Swampert
21. Lileep
22. Cradily
23. Anorith
24. Armaldo
25. Turtwig
26. Grotle
27. Torterra
28. Chimchar
29. Monferno
30. Infernape
31. Piplup
32. Prinplup
33. Empoleon
34. Cranidos
35. Rampardos
36. Burmy
37. Mothim
38. Wormadam
39. Hippopotas
40. Hippowdon
41. Patrat.
42. Watchog.
43. Basculin
44. Tirtouga
45. Carracosta
46. Karrablast
47. Escavalier
48. Shelmet
49. Accelgor
50. Tornadus
51. Thundurus
52. Landorus

Unavailable Hidden Ability Alternate Formes:

1. Pumpkaboo Small Size
2. Pumpkaboo Large Size
3. Gourgeist Small Size
4. Gourgeist Large Size
5. Flabébé White Flower
6. Floette White Flower
7. Florges White Flower
8. Floette Eternal Flower

Not released Globally:

1. Pumpkaboo Super Size(For Japan)
2. Gourgeist Super Size(For Japan)

Not released outside of events:

1. Chikorita
2. Bayleef
3. Meganium
4. Totodile
5. Croconaw
6. Feraligatr
7. Cyndaquil
8. Quilava
9. Typhlosion
10. Torchic
11. Combusken
12. Blaziken
13. Palkia(movie for Japan)
14. Dialga(movie for Japan)
15. Giratina(movie for Japan)
16. Snivy
17. Servine
18. Serperior
19. Tepig
20. Pignite
21. Emboar
22. Oshawott
23. Dewott
24. Samurott
25. Pumpkaboo Super Size
26. Gourgeist Super Size
27. Tyrunt
28. Tyrantrum
29. Amaura
30. Aurorus
31. Zapdos(for Japan and Europe)
32. Moltres (for Japan and Europe)
33. Articuno (for Japan and Europe)
34. Regirock
35. Regice
36. Registeel
37. Mewtwo(for Japan)

Edit (23.01.2015): Removed Tyrunt-line due to Battle of Hoenn competition distribution. Removed Unova starters due to global release.

Edit(03.02.2015): Removed Micle, Custap and Jaboca Berries due to recent PokéDoll Grabber PokéMileage Club attraction. Rowap Berry, which I forgot to add, is also released. Enigma Berry is also now globally available.

Edit(05.02.2015): Moved Johto Starters as they are announced to be distributed through Pokémon Bank in February 27th.

Edit(12.02.2015): Darkrai is being released in UK, and Arceus is being released in Japan.

Edit(20.02.2015): Moved Amaura-line as they are announced to be released through Dragon Cup competition distribution.

Edit(15.04.2015): Removed Dialga, Palkia, Giratina from the unavailable HA list.

Edit(22.07.2015): Removed Hoopa from unavailable Event Pokémon list.

Edit(30.10.2015):  Removed Hoopa from Global list, added Xerneas, Yveltal and Jirachi shinies.

Edit(25.12.2015): Added announced Mew and Volcanion, and added Shiny Diancie for events.

Edit(03.03.2016): Removed Hidden Ability Regis, Hidden Ability Legendary Birds, Mew.

Edit(16.03.2016): Added for Japan and Europe for Legendary Birds.

Edit(01.04.2016): Removed Jirachi normal for non-global events, removed Unnerve Mewtwo for Japan.