So during the latest Nintendo Direct, they mentioned that Harvest Moon for the GBC would be available on the 3DS E-Shop, will these ONLY be available on the 3DS, or can we get these on the Wii U E-Shop as well?

Game Boy and Game Boy Color games (like Harvest Moon) are only available on the Nintendo 3DS eShop. Game Boy Advance games will come to the Wii U eShop in the future, though whether they'll come to the Nintendo 3DS eShop hasn't been confirmed by Nintendo. Hope that helps.

That's a MASSIVE disappointment. I regret selling my 3DS now so much. Oh well, perhaps I'll grab a 3DS XL now. Been looking into Fire Emblem and I know I want Animal Crossing New Leaf (once June hits of course) anyways.