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The N64 had a lot of exclusive games that Americans wanted, but the Japanese didn't. (in general) Games that were loved in all regions sold well in all regions. Vgchartz is being a bitch at loading the games totals page so I'll go on a limb and say that Mario64, Zelda OoT and games like Paper Mario sold proportionately in japan, but most rare games are high in US/Europe.

Also, Sony is a huge japanese company, and most important 3rd parties at the time were Japanese. The biggest IPs at the time were japanese so seeing 3rd parties migrate to the PSX (for good reason) also led to this phenomenon. But it's an interesting point you raise nontheless, that Japan was much less receptive to the N64 than america was.

Here, this is kinda interesting:

Pos Game Platform North America Europe Japan Japan to US Japan to EU
1 Super Mario 64 N64 6.91 2.85 1.91 0.28 0.67
2 Mario Kart 64 N64 5.55 1.94 2.23 0.40 1.15
3 GoldenEye 007 N64 5.8 2.01 0.13 0.02 0.06
4 The Legend of Zelda: Ocarina of Time N64 4.1 1.89 1.45 0.35 0.77
5 Super Smash Bros. N64 2.95 0.6 1.97 0.67 3.28
6 Pokémon Stadium N64 3.18 1.24 0.94 0.30 0.76
7 Donkey Kong 64 N64 3.33 0.79 1.09 0.33 1.38
8 Diddy Kong Racing N64 2.91 0.99 0.89 0.31 0.90
9 Star Fox 64 N64 2.78 0.58 0.64 0.23 1.10
10 Banjo-Kazooie N64 1.87 1.13 0.55 0.29 0.49
11 Pokémon Snap N64 2.23 0.68 0.66 0.30 0.97
12 The Legend of Zelda: Majora's Mask N64 1.9 0.67 0.73 0.38 1.09
13 Star Wars Episode I Racer N64 2.31 0.62 0.14 0.06 0.23
14 Wave Race 64 N64 1.98 0.58 0.34 0.17 0.59
15 Yoshi's Story N64 1.29 0.53 0.98 0.76 1.85
16 Pokémon Stadium 2 N64 1.02 0.36 1.13 1.11 3.14
17 Mario Party N64 1.25 0.53 0.87 0.70 1.64
18 Star Wars: Shadows of the Empire N64 2 0.5 0.12 0.06 0.24
19 Perfect Dark N64 1.55 0.75 0.16 0.10 0.21
20 Mario Party 2 N64 1.28 0.14 1.08 0.84 7.71