You can take a look at my dream address for some ideas on how to set up your town.
First things first, you have to plan your path.
(also as Crunchy and Kaylee suggested, clear out all of your trees too. Now is your chance at getting a fresh start. Out with the old, in with the new!)
I started with going from all of my major landmarks, and creating a simple straight path to each of them.
This makes it easy to navigate your town, and makes it great for you to run around.
Landmarks would be your beach entrances, Roost, Town Hall, Town Square, Re-Tail, your house, and your main villager district.
Start from the landmark, and make the path go straight in, until it hits the rest of your path.
You dont really need to make a main path to every one of your villager's homes.
I'd recommend keeping it easy by planning the main path just to the district you want your villager's houses, and make smaller paths branching off to them.
Now is also a good time to consider moving any of your bridges.
Once you kind of know your main route around the town, you may find a better spot for them.
Be aware of the PWP spacing it needs before demolishing, because its a lot larger than others when first plotting.
It may not even go back into the same spot it was demolished from, if say a villagers house is right next to it.
Once you have your paths laid out, now you can find your free spaces to work with.
You can start planning out the bordering for your paths.
Its a good idea to line paths with bushes and trees, to prevent you from trampling flowers while you're running around on your new paths.
I like having bushes line the bottom, and having the trees be above the paths.
That way your view of the path isn't obscured by the leaves of the trees, and its much easier catching bugs that spawn on trees above you.
It will take a lot of playing around to get things the way you like it, so always look to revise things as you're walking around your town.
You dont have to commit to any path pattern right now, because you can always change it by replacing the pattern on the character that laid it down, which will replace ALL patterns placed on the ground with the new one.
If you don't have the QR machine unlocked yet, start talking to Sable every day. Once a day, the conversation with her progresses, and eventually she will give you access to it.
Once you have it, you can start looking online for different QR paths to use, and you can easily play around with out trying different ones, now that the patterns are laid.
Now you can start looking where you want to put your Public Works Projects.
This is all up to you how you do it, but there is a handy trick to move PWP efficiently.
You can build and demolish one thing per day, but its important to do it in this order:
1-Plan a new PWP, and put up the gyroid. DO NOT PAY IT OFF.
2-Go back to Isabelle, and demolish a PWP.
3-NOW you can pay off your new PWP, and both will be changed out come 6AM.
When it comes to new villager move ins, you should plan on plot resetting any new comers.
This will keep your paths and flower patches safe, and you can design a little residential district for them.
Look up a guide on how to do this.
As Lizzy has suggested, you can also start planning a theme for your town in terms of color.
There are countless different ways you can do this, so try lots of different things!
You wont really be 'done' in your town, but you eventually, you will run out of spaces.
Best part about locking down ALL of your spaces in your town, is that NO MORE fossils, gyroids, weeds or random flowers will spawn again.
If you are done with your fossil collection, it may be a good idea to do this.
You can also set up a dedicated space for your daily spawns, and you will have just one area to go to each morning to collect your new things. (if you do this, I suggest by a cliff, so that you can roll a chance to get a Jacob's Ladder)
Once all of your flower patches are locked, (meaning without any open spaces), you can start breeding new hybrids on your beach.
Breeding flowers on the beach is MUCH nicer, because your villagers wont add to those patches, and you can control your breeding.
You can place out 5 pairs of breeders a night, and if there is no open spaces for breeding in your main town, every pair on the beach will breed a new flower (or so).
My suggestion for anything in your town is to always look for ways to revise and make things look better.
New ideas will come to you as you are working on different spaces, so go back over older areas and see what you can improve!
Hope this helps!