I think it depends on how you play the game to be honest....A lot of people play differently and the layout reflects that.
When I pick a map, I generally don't care what my native fruit is because I'm just going to plant a majority of the fruits I want regardless. But some people care about the fruit, the grass patterns, and cosmetic things like that.
My only priority because of how I play is Re-Tail being near the pier so I can sell bugs from the island quickly.
Just to take this post as reference: I care about native fruit just because of perfect fruit, since I only have other fruit trees for completeness. My personal favorites are probably apples, peaches and cherries, in that order, since perfect pears and oranges just look very plain.
This shows grass pattern by season, which can be important, mostly because of winter, since your default shape will change into a different shape. If you're going to have a town you keep in a certain time, for instance to have permanent cherry blossoms by keeping your town in April, it probably won't really matter to you.
Re-Tail is also a personal choice. Having it close to the beach definitely makes sense for selling bugs (I don't think I had thought of that when resetting), but you could also have it close to the train station if you plan to sell lots of turnips or invite people over to sell them, for instance.
Other things I care about are town plaza and town hall placement. My current map has a really nice town hall placement, and my previous map had the town plaza right in front of the town hall, which was a pretty awesome placement imo.
Also, make sure you have enough space for everything. I avoid small strips of land, since they're hard to landscape, and having permanent structures too close together, since that also gets in the way of landscaping. I think I avoided "secret" beaches you had to swim to, as well, since that sounds like too much of a hassle for me.
As for water, it really depends on what sort of person you are. I don't mind having a large river, but I don't want to have too many ponds since they're hard to landscape, especially if you have a ton of them. There are people who prefer smaller rivers, though, so they have more land to work with.
Additionally, I don't know how you plan your layout (or plan on planning), but I usually make an Excel sheet and map out the entire town, tile by tile, then start landscaping with that.
Part of the problem you might have, though, is that the update changed things. For instance, rocks can actually be used, so that might be something to figure into your planning - in a way, they might have gotten worse to work with, if you want to work with the fact that you can sit on them.
Thank you
