I have to say, as a game programmer, I can seriously appreciate what Game Freak did with the 3D models. How they avoided faceting is amazing, and the long skinny bits look great (both are very hard to deal with). I've heard some people get stuttering etc, but I haven't been able to get that to happen. It may be related to additional hardware settings or variations, I'm not sure. I have a first run USA blue 3DS. I can understand how pushing the limit of special effects, animation rigs and polygon counts could under the most extreme conditions cause a bit of frame rate interference, but I'm honestly surprised that I don't see it happening.
As to the lack of Stereoscopic 3D all over, I can think of several reasons for this. The first is that you can't easily hide a well shaded 2D plain version of an object in the scene like you can normally, That means full 3D models for EVERYTHING. Second, if everything is a 3D model, you have a lower limit of polygons per object, and that means they don't look as good, or you end up limiting how many things show on the screen and it ends up a sparse world. Third, if this game was started before GameFreak learned about the 3DS, they would have to redo anything that didn't account for stereoscopic 3D and since the optimizing tricks I mentioned earlier get used most in over worlds, it would be a pita to redo everything. Fourth, every region that pushed the graphics processing limits would need to be carefully optimized in order to make it safe to run in stereoscopic 3D. This is very time consuming and would have pushed the release date back by quite a bit. And finally, for all the hassle that goes into making flawless stereoscopic 3D, people have to turn it off at least part of the time to give their eyes a break, and chances are they will do it in the over world... so why put a bunch of development resources into something people don't really care about, instead put them in the parts people want to see, the battles!
Remember, when it gets to a high level of quality, throwing more people and money at a game won't help... and even adding more time is limited in the results it ives. What it really takes is the time of specific individuals with incredible talent, and that is always a highly limited resource.