I would agree that we should just use the console friend code in theory...
But, with the relatively small maximum friends that each game has, you may not necessarily want the same circle of people for each game. For example, if I had my Wii console friends list maxed, and then I bought a game that no one on my current wii console list had, I would want the option of going out and getting new people for just that game.
I think the best solution would be to leave it as it is now, with separate friend codes for separate games... BUT allow for friend-codeless addition to in game friends list via the wii message board and your wii console friend list. Hell, automate the whole process so people on your console list will be auto added, but you could also use game unique friend codes to add people not on your console list.