I've had a hypothesis that the strategy was twofold. One, Nintendo is always keenly aware that younger people are going to be the audience for gaming, so utilizing older games to kids that might not have had an SNES (or at least all the prominent releases in the library) allowed them to effectively make more money off such legacy titles. In an era before Virtual Console, NES/SNES Online, etc ports like this were the most practical way of getting old games to new fans.
Two, it's worth noting that many franchises were experimenting in various ways on Gamecube; some more successfully than others. With Metroid going first person, Zelda being cell shaded, Mario Kart trying Double Dash, Kirby with only an Air Ride spin-off, Star Fox venturing into LoZ gameplay, DK attempting sigh Bongo Controllers, and even Mario bit out there with FLUDD? Playing things a bit conventionally with the GBA releases via ports/remakes might have been Nintendo hedging their bets; even if certain fans didn't like the new direction on home consoles, there were portable games that could be more to their tastes.