The latest Kojima Productions Report talks a bit about the potential Metal Gear Solid: The Naked Sample Nintendo 3DS game. Kojima Productions and Hideo Kojima are definitely interested in hearing your feedback on the possible Nintendo 3DS game.
At this point it doesn't sound like there is anything concrete on the Metal Gear Solid 3DS game, since Kojima Productions wants to hear what fans want the setting to be. Do you like the Metal Gear Solid 3 setting? Would you get a Nintendo 3DS for this game? What do you want to see in it? Make sure to let Kojima Productions know, because they're weighing in feedback on whether the game is being made and in what setting!