Without a doubt I would prefer a 3D game. Afterall, it would be more visually appealing, which of course, makes it easier to stay into the game. However, like most Mother/Earthbound fans, I think we just want to see a new Earthbound released. From the articles that I have read (mostly on starmen.net), it seems like the reason that the sequel was NOT released was mainly due to producers' inexperience with 3D.
This series is not known for its graphics, but for its storyline. As long as the storyline is great with some semi-decent graphics, I believe that all of us, as Mother fans will be satisfied. Yet, Nintendo might know this, but it isn't their job to just satisfy us, but also reach and have other people try the game out. Great reviews aren't enough, to attract people that have never heard of the game before, great visuals are almost neccessary.
My fanthoughts are as follows. If it does come out on the Gameboy Advance, the same graphics as Earthbound/Mother 2 would suffice. However, if it does come out on the GAMECUBE I don't want them to work on an all 3D game if it increases the chances of the game getting cancelled. Instead, I would like to see some graphics close to what was shown in "Harvest Moon 64." It looks nice and shouldn't be anywhere as difficult as a 3D game. And if Nintendo doesn't believe that is enough, just throw in some FMVs (Full Motion Videos) to spice it up.