Decide how complex you want your main path/road. Most paths are 1-3 tiles wide, but you can make them as large as you want. Larger paths generally give your town a more open feel whereas long single paths winding around trees and such can create more of a forest feel. You can obviously mix them up - just be aware that the wider, more complex paths can take 8++ QR slots. It takes me 3 characters to hold all the patterns just for 2 paths, but I prefer complex ones with corners and borders.
Make them practical to connect all major areas of your town. I dunno how much you want to do this, but you can control where villagers move, assuming you have the patience to path your entire town (you can go back and delete path sections after they move in).
Spend some time on QR blogs (JP ones are great. Mix up paths to create a unique personal town, but make them complement each other. For example, if you're using light green grass QR and want to add flowers, choose those that have similar grass tones.This is a long list of various QR blogs:
http://merongcrossing.tumblr.com/post/78720957620/japanese-animal-crossing-qr-codediary-blog
Have a general idea of what you want your town to be like. Instead of placing a bunch of random PWPs, try to make them go together to create gardens, parks, residential areas, etc etc. You can place the Zen Garden, Balloon Arch, and Sphinx next to each other if you want, but it won't look good XD
Also, to address your problem of things being too neat vs natural, try incorporating both

In my residential section, things are very neat and organized and perfectly placed. I add plants to give it some depth. However, I'm working on a large garden in another part of my town that doesn't use any of my main paths.
My last tip is I highly recommend creating 1-3 other characters and unlock their QR slots. If you delete them, your paths disappear, so think about where you want to place the house carefully.
Idk if any of this helped
