The Wii U version of Balloon Fight plays just like the original, except for some standard additions to Virtual Console versions of games, which do not affect gameplay in any major way.
The main addition is the ability to save and load at any point with Restore Points, which was completely impossible in the original version or the previous re-release on the Wii. Tapping the gamepad screen or pressing ZL or ZR will open up the Virtual Console Menu, which allows the player to reset the game, save or load Restore Points, change the controller mapping, or change which controllers are treated as player one or player two. Some people have also noted that the colors seem darker than normal, which in some cases can make the game difficult to see.
50Hz Vs. 60Hz Edit
Balloon Fight was one of many Virtual Console games that had different game speeds depending on the region. Because originally the games ran in 60Hz in the U.S. but 50Hz in Europe, the Virtual Console versions were different between regions to simulate this, making the European version slower. There was public backlash over this choice. Oddly, the 3DS version does not have this regional difference.