This is easily my favorite thread of the month.
I have a 3DS XL and have no intention of selling it in order to reduce the cost of the N3DSXL upgrade. Therefore, for me, this move is fine. I don't have to worry about buying a charger or having an additional one I don't need.
For those that don't already have a charger, the box is clearly labeled. This means they should notice that and buy a charger at the time they purchase the system.
Those that think a box redesign/resize, the shipping weight increase, the production time increase, and extra time spent QAing the product to make sure it is fully functional is "pennies" for Nintendo don't understand how manufacturing and shipping works, that's fine.
This is the exact same thing as a toy coming with the "batteries not included" tag. Backlash is expressed and expected because the consumer has to change the way they approach the purchase. Ultimately, you are going to be paying the same amount for the system and a charger in two separate boxes as you would've for the system and charger in one. Unless of course you buy the charger from someplace like Amazon, at which point it is actually a cheaper entry point for you.
The fact that Nintendo is being upfront about this change is a good thing. Imagine how people would've reacted if they didn't know this a month in advance?