Be cause i know it will eventually come up, they would not actually be losing money and could even charge slightly less considering two purchases.
Consider the industry marketplace:
A game is sold to gamestop for ten dollars or so less than retail. Of the profit, another 10-15 goes to the platform manufacturer; aka sony ms ninty.
Shipping and packaging is another 3 or so.
So in the grand scheme of things the revenue by a dev for one ps3 game and one vita game is:
60-(10-15 retailer)-(10-15 console owner)-(3-5 associated costs)
And
40or50 - 10to15 - 10to15- 3-5
For a total negative loss of between 46-70 of between 100-110 revenue.
Conversely, a bundle would have loss of between 23-35 of 75-80 revenue.
In both cases they will make just about the same amount give or take a couple bucks.









