It's like Donkey Kong... which version is the best? The 1994 Gameboy version. It takes the original arcade game and expands upon it. So what it has fewer colors and lower end graphics (though it does have Super Game Boy enhancements). It's the ultimate version of Donkey Kong.
I love GBO Donkey Kong, too, but it’s a very different game than arcade DK. If you take, for instance, SMB2 SNES and compare it to SMB2 GBA, these are effectively the same game—sure, there are some differences, but anyone with any familiarity with either will immediately recognize the other. And a few minor changes, even if we assume they’re universally superior, are not going to make up for the screen crunch going on in the GBA version. The graphic tiles are the same resolution, meaning SMB2 GBA, due to the GBA’s lower screen resolution, cuts off a lot of screen information that would have been visible in SMB2 SNES, which is pretty far from ideal. That’s the biggest problem, but the washed out colors and GBA’s poor sound do make a significant impact on games where the audiovisual presentation makes up a significant portion of the charm.
Don’t get me wrong, the GBA Super Mario ports are well done (look at the GBA Sonic the Hedgehog port for an example of a poorly done 4th gen platformer conversion), but claiming they’re “clearly superior” to the originals seems pretty disingenuous.
Also for the record, the GBO featured a superior CPU (Sharp LR35902 clocked at 4.19 MHz, based on the Zilog Z80) to the arcade Donkey Kong (which used a 3.072 MHz Zilog Z80), and while graphical aesthetic is subjective, I’d say that the graphics for the GBO DK are significantly better than the arcade, thanks in part to the superior hardware (which, granted, is limited to four-color grayscale) and nearly 15 years extra experience in pixelart that Nintendo possessed at that point.