Play any Mega Man Zero on an emulator with a resolution that differs from the GBA. All it does is that it stretches the graphics to fit the new screen dimensions and gameplay is not altered. With game development, when you set fixed scale and position for an object, it can be recalculated whenever the resolution changes.
Of course, I'm probably not the right person to talk, as I know nothing about the game's core programming (there MIGHT be some small things that are GBA-resolution dependent). But it shouldn't be a hard task for DS to stretch the images to fullscreen. The gameplay at core could play with the original aspect ratio, but it's just presented in bigger size (and that's basically what happens with the emulator example I mentioned). If not else, they could provide the option to choose wether to use the GBA dimensions, or "full screen".
I'm not saying Capcom's choice is the worst ever, but it just feels a bit like the rest of the screen goes to waste. Especially considering the dimensions on DSi XL's screens.