The "pop out" effect is simply a factor of the offset between points in the right and left eye images. It has nothing to do with limitations of the hardware.
Anyone who's actually experimented with the 3D camera should already know this.
Higher offset between foreground objects results in a stronger projection effect. Of course, this is simply the effect of human perception; no commercial display actually projects light to form images and frankly, anyone expecting formed light images to come shooting out of the 3DS display was either kidding themselves, or simply doesn't understand the science of how stereoscopic images work.
The downside of relying to heavily upon this "pop" effect where foreground objects are significantly offset between left and right fields is that they are taxing on the eyes. Try holding both index fingers about 4 cm apart and adjusting the focus of your eyes so that they appear to converge as a single finger. Maintaining that focus for extended periods of time does strain the eyes.
As for the whole cost issue; it really isn't. Nintendo only priced the 3DS at $250 because they determined that's what they could sell the device for to early adopters. The BOM is about $100 and the Sharp parallel barrier display adds about $10-15 to the unit cost; hardly anything worth making a big deal out of.
For that little amount, it doesn't matter whether the 3D effect is even well implemented by developers or used by the consumer. The success of the platform will still be dependent upon the eventual quality and quantity of the software library.
"Glasses Free 3D" may be the biggest marketing bullet for the 3DS, but it is pretty far from being the only feature that distinguishes it as a new platform.
