I find it funny how Paper Mario is now considered one of the N64's best games, but back then it was too I am a terrible poaster. for its own good...
In 10 or 20 years people will hail Wii Music as a brilliant masterpiece. Quote me on this...
I recall it being regarded rather fondly at the time. It gets an 88.5% rating on GameRankings which is very respectable. Anyone who crapped on it at the time was usually someone who just crapped on the N64 period. It was Sony fanboys who thought it was for kids. But Nintendo fans and most reviewers thought it was great.
Wii Music on the other hand got mostly negative reviews and gets crapped on by many Nintendo fans and Wii owners. I don't think it makes sense to compare it to Paper Mario's reception. Paper Mario was just another misunderstood masterpiece at a time where anyone who didn't specifically follow Nintendo wrote them off and at that point any Nintendo console game was getting written off. If anything it was unknown or ignored more than crapped on. If Wii Music is later regarded as a misunderstood classic that will be very exceptional. It is much more unpopular than almost any other Nintendo game. It is not a wallflower game, it's outright infamous.
Here are how the Wii Music reviews. The bad reviews come mostly from core media outlets who only saw the game as a noise maker with no depth (IGN, Game Informer, Game Daily etc.). The good reviews, however, come from outlets who saw the game for what it was and claimed to have depth for those willing to look for it (1up).
Like Golden said, it has received mixed reviews, but that's to be expected. Wii Music is a niche concept game, and those games either get a lot of love or a lot of hate.
Wii Music actually receives praise from the fanbase. There are a lot of videos on YouTube, and there are communities dedicated to the creation and sharing of videos, and those fans saw depth that not even Nintendo foresaw.
So the reason why I say the game will be fondly remembered in a few years is because it has gained a loyal fanbase that will sing its praises, and chances are that those gamers will become journalists and help propel a good image of Wii Music.
This has happened with cult movies, songs and artists, and of course videogames.