It comes down to the strength of the competition.
The GBA succeeded because Nintendo had (and still has) the handheld market on lock. The GBA was affordable and had all the right games needed to prove to be a hit system. At that point, the most successful non-Nintendo handheld had been the Game Gear, which sold fewer than 11M units worldwide. The GBA was running effectively unopposed. It had a strong performance in Japan, putting up the second-best single-year performance ever for a system at the time in 2001. It did especially well in the U.S. It managed to beat the PS2 as the best-selling system of the year in 2003 & 2004. In fact, by the end of 2004 it had managed to almost catch up to the PS2 in LTD sales in non-aligned terms despite releasing eight months later. It was by the end of its short life the third best-selling system ever in the U.S. at the time, behind only the PS2 & Game Boy. While it was later knocked down a few ranks by the DS, Wii, 360, & Switch, it managed to put up sales during its prime that were among the best ever. If it had a couple of more years before the next generation of handhelds released, it probably could have passed 100M units sold worldwide.
Meanwhile, the GameCube did relatively poorly because it had to contend with the strongest competition Nintendo ever had. It had the misfortune of coming off the heels of the N64. Nintendo already lost a ton of market share in the previous generation, for reasons already discussed to death. The PS1 easily won its generation, outselling the N64 three-to-one worldwide. The PS2 was riding the wave of that momentum, going into 2001 with its only competition being the Dreamcast, which it was outselling by staggering margins. The GameCube not only released in the face of competition that was already that dominant, it also had to contend with Xbox. That generation's outcome was already settled before it got fully underway, and the PS2 consistently maintained majority market share. Basically, it was Nintendo vs. Xbox in a race to determine who would take the spot of a very distant second place. Xbox ended up edging out the GC worldwide, mainly because of a relatively strong performance in the U.S.
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