I think it would be wise for Nintendo to offer a good selection of cheap, quality, digital-download games (and the 3DS eShop is already doing a decent job of this) to grab the iOS crowd, but their full-price franchise retail games aren't going anywhere. Nintendo's been able to consistently sell Mario and Zelda games on Wii at $50 for years and years, when every big game on competing platforms usually drops to around $30 within months. The 3DS picked up steam when they slashed the hardware price, but they left the $40 standard software price intact (even though I think that's way too high) and it seems to be working just fine for them.
I wouldn't bet on Wii U games going for $60, either. Nintendo seems to recognize that $50 is the magic price point.
And yeah, I think even the most casual, 99-cent gamer recognizes the difference in depth of experience between say, Arkham City Lockdown and Arkham City. There's rooms for both types of gaming and they'll continue to be priced accordingly.