DS Version vs. 3DS Version
The Tale of Two Towns is being released on two consoles. There is a Nintendo DS version of the game and a Nintendo 3DS version of the game. The same game is on both consoles, but the 3DS version has a few enhanced features. You'll find the same characters and storyline in both versions of the game.
The DS Version is not Region Locked
Many fans of Harvest Moon outside of North America prefer to buy the Natsume release of the game instead of waiting months (or years) for the game to be released in their country or region. Nintendo DS games are not locked to a specific region and can be played on any Nintendo DS or 3DS video game console. The DS version of The Tale of Two Towns is a standard region-free DS game and can be played on any country's console.
Nintendo 3DS games, on the other hand, are region locked. If a player has the North American 3DS version of TToTT, then he/she must also have a North American Nintendo 3DS console in order to play the game.
The 3DS Version Has 3D-Enhanced Graphics
Both versions of the game look identical in a non-3D mode, but the 3DS version has been improved with 3D features on the top screen. The stamina bar and conversation dialog boxes pop out of the 3D screen on the Nintendo 3DS whereas on the regular DS console the same features are flat.
The view of the world has been widened to take advantage of the 3DS' wider screen resolution. A standard DS game displays in 256x192, but a 3DS game displays in 400x240. Instead of stretching the DS game to fit the 3DS' wider screen, the game has been adjusted so the "view" of the world is wider. The conversation dialog boxes are still in the middle of the screen and have been adjusted to take advantage of the higher resolution
If you mainly play your 3DS games with the 3D disabled, the only benefit is you see a wider top screen. It won't give you any advantage when playing the game.
The 3DS Version Has Street Pass
One of the features of the 3DS is that you can transfer data between other 3DS consoles as you walk by other 3DS players. Street Pass allows you to receive extra rewards in 3DS games. The 3DS version of Tale of Two Towns supports Street Pass, which allows you to put items in your Street Pass Box that can be transfered to other players who walk by. The Send and Receive boxes support up to 12 items each.
The 3DS Version Has an Extra Petting Mini Game
Similar to the petting game from Island of Happiness or Sunshine Islands, the petting game in TToTT will allow you to rub your animals to make them happy. The better your score, the more bonus friendship points you'll earn. This means there is an extra way to increase your animals' hearts in the 3DS version that doesn't exist in the DS version, making it faster (and easier) to max out their friendship hearts.