I think the bigger problem lies in Nintendo not being willing to let other companies handle their IPs, in the vein of Retro Studios or Rare (and I guess Intelligent, though all they really do is RPGs). There's simply no way that a single developer, even one with as many resources as Nintendo, can consistently create games for two dozen different IPs. Right now, it's a story of opportunity cost more than anything. Something like a 2D Metroid or a Mother title would be incredibly cheap and almost certainly turn a profit, but spending development time on that means ignoring creating a title for something else that would be more profitable.
Find some medium sized developers like Platinum or Koei Tecmo (both of which Nintendo has decent relationships with) and let them take a stab at revitalizing older games. That way, Nintendo can still focus on its more profitable titles/new IPs while giving fans of smaller series something to look forward to. Even if it doesn't turn out to be amazing, the series was going to just sit there anyway.
I'd argue that, above all else, the real issue is Nintendo being overprotective of its IPs...which is consistently becoming a common theme. Certainly don't hand series off to whatever publisher wants to do something with it (and possibly restrict Team Ninja's ability to design Zelda villains if you do), but if the franchise is just collecting dust, then why not take a few more shots?
