Zelda Spirit Tracks and Phantom Hourglass > Minish Cap (even if PH does so only barely)
Mario Kart DS > Super Circuit
Mario Party DS > Mario Party Advance
GBA doesn’t have a real Mario platformer of it’s own and DS had Professor Layton. I admit I stupidly missed Metroid and Fire Emblem, which were excellent, on GBA but that was because I had already given up on GBA (and GC) at that point.
DS was better.
If however you’re including the many ports on GBA it makes a much stronger case because then you’ll have to consider A Link to the Past, Yoshi’s Island and Super Mario Bros. 3. Is DS still better then? Not sure.
3DS and GameBoy beat both though, no contest there.