Do you realise the 3DS renders at a higher resolution than the DS, not to mention a massive boost in the horizontal aspect ratio?
this is a rough comparison of the resolution of the 3DS and DS's top screens:
The resolution boost is much greater than the boost from the GBA to the DS, and that prompted a complete graphical update of the games. Not to mention the 3DS can pull out far greater polygonal graphics than a DS can, and has about 24 times as much memory as the DS.
Instead of stretching the graphics to fit the new resolution (which I agree, that would be ugly), couldn't they just enlarge the viewing area? In other words, you'd be able to see Zoroark's feet and the tip of its ponytail in the 3DS version of that screenshot? I wouldn't know, I'm not a programmer.
What you're suggesting is the laziest thing I've ever heard and even I don't believe Nintendo and Game Freak would stoop so low as to repackage a DS game. Hell, the Zelda remake gets enough ire for looking kinda sub-par in the face of what other companies are producing for the 3DS, and development of that one was outsourced (and still looks noticeably better than the N64 original).
Sir, the Pokémon franchise is famous for being lazy. Yellow, Crystal, Emerald, Platinum, and the Japanese Blue were all built with pre-existing software. However, the idea of Gray being for the 3DS sounds less lazy to me than any of the other third versions. Before, they were releasing basically the same game on the same console twice (thrice if you take into consideration that the first release was split into two versions). In this case, they would be releasing the same game onto two different consoles, which is the fate of most video games once you think about it. Take Madden '07 for example: it was released on PlayStation 2, PlayStation 3, PlayStation Portable, Xbox, Xbox 360, Windows, DS, Game Boy Advance, Wii, and Nintendo GameCube. It's not lazy, it's smart.
As for the graphics being under par, it wouldn't be the first time. Look at the generation 4 games. The halved frame rate along with the awkward pseudo-3D make it look worse than generation 3, in my opinion. And the aesthetics of the battle system didn't even change between the two generations!
(I'm also pretty sure that Game Freak wants to get to grips with the 3DS as soon as possible so they can come out with as polished a game as possible roughly 2 years into the lifespan of the 3DS, like DP was to the DS)
I agree with this, though I still think Gray will come for the 3DS first unless the graphics don't transfer well to the heightened resolution as you suggested. As for the Ruby/Sapphire remakes everyone has been hyping, I don't see them coming out until after the third version of generation 6, if at all.