Hi there. I read your post with interest as I had a similar experience with the nikonD3100. I owned a d5000 and unfortunately it was stolen. My insurance replaced it with the 3100 and my shots were not reliably clear. I am a stickler for clear eyelashes in portraits and I take pictures of my kids most often. So, after lots of work I came across a post by Wolfgang Spekner who was very pleased with his photos straight from the camera (JPEG). He said he used in camera sharpening set at "+7" and saturation "+1". I figured out how to get to that menu (go into vivid mode) and I increased sharpness. It seems to have worked wonders. The in-camera sharpening made all the difference (more reliable, clearer pics).
Let me know if it works. I still need to print mine to check it out on paper!