Thank you to u/CalmBrony for the initial groundwork with their own list.
Micro Series was later republished as Pony Tales.
Comics marked 'TBA' don't have titles yet. If you have said titles, let me know.
The following reading list aims to preserve the original publication order as much as possible, while not breaking up story arcs:
Comics from 2013:
FiM #1-4 (The Return of Queen Chrysalis)
Pony Tales #1: Twilight Sparkle
Pony Tales #2: Rainbow Dash
FiM #5-8 (Nightmare Rarity)
Pony Tales #3: Rarity
Pony Tales #4: Fluttershy
Pony Tales #5: Pinkie Pie
Pony Tales #6: Applejack
FiM #9-10 (Zen and the Art of Gazebo Repair)
Pony Tales #7: Cutie Mark Crusaders
Pony Tales #8: Princess Celestia
FiM #11-12 (Neigh Anything)
Annual 2013: Equestria Girls
Pony Tales #9: Spike
FiM #13-14 (My Little Pirate)
Pony Tales #10: Princess Luna
Comics from 2014:
FiM #15-16 (The Book Worm)
Friends Forever #1: Pinkie & Applejack
Friends Forever #2: CMC & Discord
Friends Forever #3: Celestia & Spike
FiM #17-20 (Reflections)
Friends Forever #4: Twilight & Shining Armor
Friends Forever #5: Fluttershy & Zecora
Friends Forever #6: Rainbow Dash & Trixie
FiM #21-22 (Manehattan Mysteries)
Friends Forever #7: Pinkie & Luna
Friends Forever #8: Applejack & Rarity
FiM Issue 23 (Pets to the Rescue)
Friends Forever #9: Granny & The Flimflam Bros
Annual 2014: Power Ponies
FiM Issue 24 (Discord in Time)
Friends Forever #10: Fluttershy & Iron Will
Friends Forever #11: Rainbow Dash & Spitfire
FiM #25-26 (The Good, the Bad and the Ponies)
Friends Forever #12: Pinkie & Twilight
Equestria Girls Holiday Special
Comics from 2015:
Friends Forever #13: Rarity & Babs Seed
FiM #27-28 (The Root of the Problem)
Friends Forever #14: Luna & Spike
Friends Forever #15: Applejack & Mayor Mare
FiM Issue #29 (Ponymania XXIX)
FIENDship is Magic #1: King Sombra
FIENDship is Magic #2: Tirek
FIENDship is Magic #3: Sirens
FIENDship is Magic #4: Nightmare Moon
FIENDship is Magic #5: Queen Chrysalis
Friends Forever #16: Diamond Tiara & Silver Spoon
FiM #30-31 (Ponyville Days)
Friends Forever #17: Twilight & Big Mac
Friends Forever #18: Rainbow Dash & Fluttershy
FiM #32-33 (Night of the Living Apples)
Friends Forever #19: Rarity & The Cakes
Friends Forever #20: Luna & Discord
FiM #34-37 (Siege of the Crystal Empire)
Friends Forever #21: Spike & Zecora
Friends Forever #22: Celestia & Pinkie
Friends Forever #23: Applejack & Fluttershy
My Little Pony Holiday Special
Comics from 2016:
Friends Forever #24: Rarity & Gilda
FiM #38-39 (Don't You Forget About Us)
Friends Forever #25: Rainbow Dash & Twilight
Friends Forever #26: Shining Armor & Prince Blueblood
FiM Issue #40 (Twilight meets Spike)
Friends Forever #27: Pinkie & Granny Smith
FiM Issue #41 (Rainbow Dash and the Very Bad Day)
Friends Forever #28 Princess Luna and the Cutie Mark Crusaders
FiM Issue #42 (A Pinkie Pie Story That Pinkie Pie Kinda Sorta Remembers)
Friends Forever #29 Rarity and Maud Pie
FiM Issue #43-45 (Ponies of Dark Water)
Friends Forever #30 Twilight Sparkle and Princess Cadance
Friends Forever #31 Rainbow Dash and Little Strongheart
Friends Forever #32 Fluttershy and Daring Do
FiM Issue #46-47 (Election)
Friends Forever #33 Applejack and Cherry Jubilee
FiM Issue #48-50 (Chaos Theory)
Friends Forever #34 Pinkie Pie and Cheese Sandwich
Friends Forever #35 Twilight Sparkle and Starlight Glimmer
Comics from 2017:
Friends Forever #36 Rainbow Dash and Soarin'
Friends Forever #37 Rarity and Trixie
FiM Issue #51-53 (From the Shadows)
My Little Pony: Guardians of Harmony Annual 2017
My Little Pony: Deviations
Friends Forever #38 Princess Celestia and Princess Luna
FiM Issue #54 (TBA)
FiM Issue #55-56 (Wings Over Yakyakistan)
FiM Issue #57 (TBA)
FiM Issue #58 (TBA)
FiM Issue #59 (TBA)
FiM Issue #60 (TBA)
FiM Issue #61-62 (Convocation of the Creatures!)*
My Little Pony Holiday Special 2017
Comics in 2018:
FiM Issue #63 (TBA) - February 2018
My Little Pony: Legends of Magic Annual 2018 - April 2018
FiM Issue #64 (TBA) - March 2018
FiM Issue #65 (TBA) - April 2018
*Issue 62 releases January 31, 2018.
