I mean, most of those exclusive 3DS games were Unity shovelwares, and a lot of "exclusives" DSiWare games were re-packaged DS titles.
From the Iwata asks of the "exclusive" Brain Age DSiWare games
They also repackaged for digital distribution Electroplankton, 42 WorldWide games and other titles. They weren't new games, they were the old games sold in digital chuks. GBC on the other hand had Resident Evil, Dragon Quest, Rayman...
But even without looking at the kind of the exclusives, GBC games replaced GB games. In late 90s/early 00s
nobody, from Nintendo to a smaller-scale European publisher, was producing GB games anymore. Everything was only for GBC. In layman's terms, the major difference between GBC and DSi/n3DS is that Oracle of Ages/Seasons couldn't be played on OG GB, whereas Spirit Tracks and Tri Force Heroes could be played on launch-day DS and 3DS.
A better comparison for DSiWare and 3DS exclusives could be the Famicom Disk System or the Satellaview. When the FDS was released, they still produced Famicom games, but there were also FDS exclusive games. The FDS was an
extension of the Famicom platform (which also offered hardware enhancements), not a replacement. Due to the handheld nature of DS and 3DS, their extension was also a hardware revision. The GBC, on the other hand, effectively replaced the GB.