To put this simply, Sony is upset with Nintendo’s marketing of the 3DS because it will (likely) act like a poison pill for Sony’s efforts in promoting shutter-glasses based 3D. While there are some cosmetic and comfort reasons why people dislike 3D glasses, there are also many practical reasons why people don’t like them; including that they’re expensive, and you might need 16 pairs of glasses if you ever wanted to host a super-bowl party (and I doubt the glasses are going to conform to a universal standard).
Sony has spent a lot of money in R&D towards this technology, and is currently spending a lot of money marketing the approach, and their hope is that they can convince people that 3D is so cool that they can live with the down-side involving 3D glassesl. If Sony can't convince consumers to buy into their approach they will lose a lot of money; and they will be years behind the competition in developing the desired technology, and will probably be forced to licence it.
With the 3DS Nintendo is giving people the 3D experience they want without the usual downsides that they associate with 3D, and even the limitations of their 3D display are not going to be significant with their system; basically, there is supposed to be a sweet spot for the 3DS display which prevents it from being used by multiple people but on a portable system that isn’t much of a concern.
If/when the 3DS is successful and Nintendo convinces people that 3D glasses are a major problem Sony stands to lose billions of dollars. To make matters worse, without significant sales of 3D displays Sony’s efforts to rebrand the PS3 as a 3D console will be completely irrelevant, and any boost Sony gets will be negated.










