I agree that not continuing to make Wavebirds was a stupid move.
However, I have to imagine that Nintendo wants to get away from the GC image. GC, in the minds of many people, was a failure. Also, they probably don't want people to connect that they're playing their 'brand new next gen system!' with an old controller. It seems silly (especially considering that Sony has done it for about a decade now), but it makes sense for marketing purposes.
They want you to use Wii accessories on your Wii console. They aren't pushing BC, it's just a nice bonus.
Now... let's even just look at it from a monetary point of view. Would Nintendo rather you buy a $35 Wavebird... or a remote and CC set that's going to run you $60, total? I mean, really... look at Smash Bros... think about how much money there is to be made just on controllers ALONE for that game. It's a 'party' system, so people will need more than one or two controllers... so might as well force them to buy the most expensive possible, right?
... and, you notice that RE4 made no real mention of the Wavebird support, right? Has to be a reason.