This might be a side effect of searching "top 15 3DS games" and going from that list. Most of them are filled with JRPGs, and JRPGs on the 3DS surely do love to use the chibi artstyle - the 3DS can't handle that many polygons at once, so simplified models make sense, and a chibi artstyle fits the genre and most of the target audience.
But there are plenty of counter examples of games that might not make the list, but have their own style. Though yes, most will have simplified geometry. Let's see:
Monster Hunter 4 Ultimate
Resident Evil Revelations
Metroid Samus Returns
The Legend of Zelda: A Link Between Worlds and The Legend of Zelda: Ocarina of Time 3D
That's a good point. Must be the low resolution. Have you tried Xenoblade Chronicles 3D? I'm curious to hear what people think about the style of that game on the New 3DS
The low resolution doesn't bother me. The fuckin chibis do. Xenoblade was alright but I didn't get far because the combat bored me, I do plan on going back to it soon though. I just hate the tiny bodies and big head character design in most games. Phantasy star 0 for the DS had a low resolution but still looks better than any rune factory game because they aren't chibis