The SNES and DS versions also run at different aspect ratios (but almost the same resolution). The SNES is 4:3 with non-square pixels, so the DS version looks thinner. This exaggerates the effect of the DS version’s thinner font even more.
I always felt like the DS version was harder to read; looking at them side by side, I see I wasn’t making things up! The SNES version’s font genuinely has bolder lines that are a bit easier to read.
@pobocks Yeah, no kidding! I guess it makes some sense; if it was designed as a menu font on the GBA to save screen space, it's going to be super compact. But that doesn't mean it's the right choice when you've got plenty of screen space available...