Ooh, the fun of a blank canvas town! All the possibilities!
The first thing would be to determine what kind of feel you want for your town. Woodsy, natural? Urban, city? Dark, gothic? Maybe pastel, kawaii? You get it. Then determine where your major PWPs will be (I used throw-away pattern markers to block it out) and start figuring out the traffic paths to get you wherever you need to be. Probably one going down from your house, over to Town Hall and the Plaza, a branch off that for the beach ramp, over to Re-Tail, up to the caf?, etc.
Once you have that, pick a section. I found that trying to work on my entire town, all at once, was too overwhelming. Maybe start under the waterfall, where you have some permanent structures already set. It's easier to landscape around something, rather than try to put all the pretties in and then build. I used specific bushes and flowers in different areas, which gives the feeling of little neighborhoods in town. The overall feel is cohesive, but there are areas with their own personality.
Don't make every path straight. Put some curves in and let areas meander a bit. When you come to a curve, you can tuck a small PWP or little collection of flowers in, and it'll give you a feeling of discovering something secret. Also, vary the width of your paths. Two squares wide is comfortable, but take it down to one sometimes (works great in forested areas) or open it up to three (gives a feeling of a park).
Remember that nothing is set in stone. Well, a few PWPs are, but landscaping can be changed again and again. I thought I was about finished, other than waiting for a few specific bush types to become available. I showed my town to a friend last night, and asked her opinion on my park area - something about it was just not jelling for me. The result was a visit to Isabelle to demolish something, a dozen or so bushes dug up, flowers redistributed, and new markers laid down for bush placement. But it'll be a lot more open and make the smaller spot look bigger.
Good luck, and have fun! Don't worry too much about what everyone else thinks "should" be done in a town. If you like it, it's meant to be.