Pricing is consistent because it's decided in accordance to how much the games will sell.
For Metroid Prime, you have to remember that it had already been packaged within a trilogy in 2009 (retailed for $50 back in the day on the Wii) that was re-released on the Wii U digitally for $20. That's why $40 for a graphical overhaul seem to be the right price.
WarioWare and other party games command a lower MSRP because the $40-50 bracket has worked for generations. Titles like Big Brain Academy and Brain Age have always had the lowest tier in terms of pricing.
All the confusion stems from the false assumption that price is determined by production plus marketing budget when it's actually determined by value. And value is determined by customers.
Legend11 correctly predicted that GTA IV will outsell Super Smash Bros. Brawl. I was wrong.