If you choose to update your Virtual Console copy of this game, you'll get both upgrades and downgrades (am total).
It doesn't happen often, but some Virtual Console games are updated after their initial releases to correct various bugs. Many users of the service may not realize these updates are available, because Nintendo does not announce them or notify consumers through Wiimail or any other means. The only way you can keep abreast of the updates is to look at "Titles You've Downloaded" on the Store Channel. Games with updates available will have a small "Updated!" tab above the title. Of course, these patches are free, but you will have to download an entirely new ROM, which may take a while in the case of larger games like Star Fox 64.
Just released today, the update for Star Fox 64 corrects a major complaint about the original Virtual Console release -- that the Classic Controller's joystick was far too sensitive for this game. The updated version puts the Classic Controller on equal ground with the GameCube controller, which was previously the only way for cool people to play this game on Wii. However, you may still find the GameCube controller's button layout to be better suited for the game, and that's one advantage not likely to be fixed by a software update.
Unfortunately, the update for Star Fox 64 also unravels one of the improvements over the original cartridge release, because slowdown is back in the game. After hearing about this rollback on various gaming forums, we tested it for ourselves and found that there is definitely some slowdown in the updated version which was not there before. The effect is immediately noticeable on the planetary map screen before each level. It's the same slowdown that was present in the old N64 version, but the first VC release corrected nearly all of the game's frame rate problems. (Incidentally, the proper speed made levels such as Aquas far more difficult.)
So, is this update worth downloading? Yes, if you don't own any GameCube controllers and found the game to be unplayable with the Classic Controller, as we stated in VC Mondays a few weeks ago. If slowdown really bothers you, and you're already used to playing the game with a WaveBird, there's no need to grab the update as far as we can tell. (It's entirely optional, so if you've already downloaded the game, you are free to leave it as is.)
We also tested to see if rumble support for GameCube controllers was added. It wasn't.
We'll update this story if any other changes in the update are confirmed, but so far it's just joystick sensitivity and reintroduced slowdown. Until Nintendo starts to provide some kind of documentation for these patches, we have to rely on anecdotal reports and our own testing.