My own thoughts:
Divinity Original Sin 2 being present is awesome, but only at 98? That and Baldur's Gate II being eclipsed by Diablo II and The Witcher 3, with no Planescape: Torment on the list?
Bioshock outranking System Shock 2?
Mega Man 3 instead of 2?
SMW at #1? LttP at #2 with no Link's Awakening? Mario 64 the only 3d Mario when it's far from the best of the lot?
Also, they should have placed Donkey Kong '94 instead of the original.
Too many Grand Theft Auto games, nothing else to represent Final Fantasy or Castlevania (I've played better than SotN), and not a single Dragon Quest.
Oh God not another one of these shit lists. What's with these Journalists shilling so much for Nintendo? Are they getting a little something under the table? Anyway I'm going to rearrange some of these for the heck of it.
100. Pokemon Go <--- Seriously, is this even a game???
99. Borderlands 2
98. Divinity: Original Sin 2
97. Dishonored
96. Final Fantasy VII <-> The Legend of Zelda: Breath of the Wild (yeah... how do u like it now?)
95. Assassin's Creed IV: Black Flag
94. Monkey Island 2: LeChuck's Revenge
93. Burnout 3: Takedown
92. Fallout 2
91. Undertale
90. League of Legends
89. Mega Man 3
88. Thief II: The Metal Age
87. Soulcalibur
86. SimCity 2000
85. Inside
84. Contra
83. Tony Hawk's Pro Skater 2
82. Monster Hunter World
81. Resident Evil 2 Remake <-> Tetris
80. System Shock 2
79. Grand Theft Auto: Vice City
78. Persona 5
77. Fortnite
76. Fable 2
75. GoldenEye 007
74. Super Smash Bros. Ultimate
73. The Elder Scrolls V: Skyrim
72. X-COM: UFO Defense
71. Suikoden II
70. Battlefield 1942
69. Dota 2
68. Mario Kart 8 Deluxe (where's the better Mario Karts?)
67. Star Wars Jedi Knight II: Jedi Outcast
66. Spelunky
65. Donkey Kong (where's DKC???)
64. The Sims
63. Rock Band
62. Red Dead Redemption 2
61. Tom Clancy’s Splinter Cell: Chaos Theory
60. Super Mario World 2: Yoshi's Island
59. Silent Hill 2
58. Grand Theft Auto: San Andreas
57. Mass Effect
56. Call of Duty 4: Modern Warfare
55. Rise of the Tomb Raider
54. Batman: Arkham City
53. The Witness
52. Journey
51. Uncharted 2: Among Thieves
50. Overwatch
49. Deus Ex
48. Baldur's Gate 2: Shadows of Amn
47. Ms. Pac-Man
46. Counter-Strike 1.6
45. Left 4 Dead 2
44. EarthBound
43. Resident Evil
42. Diablo II
41. StarCraft
40. World of Warcraft
39. Star Wars: Knights of the Old Republic
38. Fallout: New Vegas
37. Final Fantasy VI
36. Mass Effect 2
35. Pokemon Yellow
34. Bloodborne
33. Metroid Prime
32. Resident Evil 4
31. Shadow of the Colossus (2005)
30. Metal Gear Solid
29. God of War (2018)
28. Witcher 3: The Wild Hunt <-> Portal 2
27. BioShock
26. Sid Meier's Civilization IV
25. The Legend of Zelda: Ocarina of Time
24. Minecraft
23. Halo: Combat Evolved
22. Half-Life
21. Metal Gear Solid 3: Snake Eater (WTF is MGS2? MGS2 > MGS3 imo)
20. The Last of Us
19. Doom (1993)
18. Chrono Trigger <-> The Legend of Zelda: A Link to the Past
17. Portal
16. Dark Souls
15. Street Fighter II
14. Super Mario Bros.
13. Halo 2
12. Castlevania: Symphony of the Night <-> Super Metroid
11. Grand Theft Auto V
10. Super Mario 64
9. Red Dead Redemption
8. Half-Life 2
7. Tetris <-> Resident Evil 2 Remake (Tetris is a classic, but better than REmake 2, I think not!)
6. Super Mario Bros. 3 <-> Super Mario World
5. The Legend of Zelda: Breath of the Wild <-> Final Fantasy VII (F you for putting VII so low!)
4. Super Metroid <-> Castlevania: Symphony of the Night (SOTN > Super Metroid imo)
3. Portal 2 <-> Witcher 3: The Wild Hunt (no way Portal 2 is better than Witcher 3)
2. The Legend of Zelda: A Link to the Past <-> Chrono Trigger (F you Zelda get off the top 10 list!)
1. Super Mario World <-> Super Mario Bros. 3 (SMB3 > SMW)
There's still A LOT that I disagree with this list and A LOT missing that should be over others, but if I attempted to recreate this list from scratch it would be a completely different list.
Only one I agree with you on is SMB3 over SMW. (Haven't played RE2Remake yet, but Tetris in various iterations, i. e. 99, Tetris Effect, TGM 3 is god tier.) Super Metroid is far superior to SotN in terms of design and ease of backtracking (so are Aria and Dawn of Sorrow), Donkey Kong Country was derivative and inferior to DK '94, and WItcher 3 has a wack combat system and far from the best WRPG. (Divinity: Original Sin 2, which by contrast had an awesome one, barely made the list, and Planescape: Torment wasn't even on the list when it should have by all rights been near the top.)