What earth makes you think that Nintendo's suddenly going to give so much a fuck about the eShop that they'll sacrifice millions of sales to "legitimize" it? It's not going to happen. The only thing less likely than that would be them announcing that they've handed their 66% of the franchise over to Game Freak, followed by GF announcing the very next day that Pokemon Gray will be a multiplat title for 3DS, PSP, Vita, iOS, and Android. We all want Nintendo to finally care about DD, but there's just no chance. The only way Gray will be on the eShop is if Nintendo starts putting retail titles there.
Also, don't you think that they might have spent the last year upgrading the graphics?