Oh boy... This is probably going to end up being a very long post, because there is a lot I can say about how I plan my towns (but I love talking about it, lol). For me it can depend on several different factors. I have three copies of the game, but right now I'm only focused on one copy. I'm getting ready to start a second town, though, so maybe typing this up will motivate me to work on it haha.
Pre-Planning Stage:
I consider this the pre-planning stage because this is typically what I do before I even make or reset a town.
1. Determine town theme (if any) - This will also determine how much planning I put into it. If I don't plan to have a theme, or I just want a carefree casual natural town then this won't matter at all.
2. Make a list of map features - This I tend to do with any town I make. There are certain things I like and dislike in my maps, so it's hard for me to overlook it. I usually note things like: River shape, waterfall position, town fruit, location of permanent buildings, location of rocks (there's a rock placement guide somewhere), etc.
3. Make a list of villagers - I don't really do Dreamies, but instead make a list of villagers I like for each personality type. Sometimes I will only pick villagers who's house exterior matches my town theme. I eventually have to narrow it down, which is the hardest part, lol.
4. Pick PwPs - I don't always do this, but sometimes I will make a list of PwP's I know I want.
5. Reset, reset, reset until I find a map. Sometimes it takes me days, sometimes only a few hours. I'm super particular about my maps, because I have a habit of resetting thinking I can find one I like better; it's easier to get one I really like from the get go, lol.
Planning Stage:
1. Make a gridded map - One of the first things I do with a new town (if I intend to plan it out in full) is to make a gridded map. I have a blank gridded map that fits the acre number and sizes for a New Leaf town, and I use Microsoft Paint to then fill squares in. I usually start at one corner of my town and dig holes, counting where buildings, rocks, houses, ponds, etc. lie on the map. Sometimes it's not 100% accurate because I mess up, but it always works.
2. Start planning! - Once I have the gridded map done (and saved, usually with a spare copy) I use that to brainstorm where I want what. I'll start with the villager houses most of the time, decide where I'd like to try plotting them, etc. I pretty much use the gridded map to plan everything, and it's not something I do and finish immediately. I work on it over time as I play the game, adding and changing things constantly. I'll put in where I want trees and bushes planted, too, but I don't usually bother trying to plot flowers.
3. Villager Plotting - Once I know where I want my villagers to go I get ready to plot reset. Since the Amiibo update I do place patterns down everyone except the spots I've decided I want my villagers. Only then do I try to being acquiring them for the town. It's much easier to do this before starting PwPs and landscaping, imo. I do plot reset, though, because sometimes I will miss a spot with the patterns lol.
Everything else?:
Honestly that's about it for the planning... I use the gridded map to decide where I want my paths to go. I like to try to make my own, but I kind of suck at it so I usually end up finding some online. I also have a habit of changing them a lot. I've only recently begun to actually farm PwP's in my main town. I used to not bother, but I haven't had as much time to play lately, so while I'm busy with something else I'll do the diving trick. My main town is set a few months back so I gradually TT day by day to do this.
I'll probably edit this if I think of more, lol; sorry for the long post!