It's just a theory, but I think what they're doing is gauging interest. Mother 1 was a very easy game to port: the translation already existed so it was just a matter of getting it to work on virtual console. That's all. I think, if it sells well, we might see Mother 3 in virtual console in the future as well. While Tomato did offer his translation, they obviously wouldn't take it: it'd need to be re-translated, which takes a lot more work than just putting the Earthbound NES prototype up onto VC.
So, as far as I figure, if Mother 1 - a game that can be emulated just as easily as Mother 3 can - has good sales and a lot of interest then maybe they'll set out to localize Mother 3. It's a lot more likely than when we were all hoping for a DS port back in the day. Digital distribution is a lot safer.