My town has three. I don't mind the ponds as much as I mind the rocks though. Right now I'm really irritated with the rock that decided to station itself next to the plaza. I didn't notice this while map planning
I noticed now when I was landscaping.
I have a trend of getting towns I love with maps I love - and they have the Town Hall pond.
At least Four of my towns in the last two years have the Town Hall pond.
I have never kept a town with the Train Station pond.
The most ponds I have ever had is four. Pixel has four and they are all out of the way - they have never bothered me and I like them quite a lot. The southern most pond has just enough space for an alternate character - I've had a few in that space over the years. I've since opened up that area so the pond is more of a natural feature.
If I am going to have an extra pond I'd most prefer the Town Hall pond.
Houston has 3, The one Italicized 8 one behind the town hall is kind of in the way of things, but nevertheless it will have to do! I kind of wish that there didn't HAVE to be a pond next to Re-Tail, it'd make Re-Tail a little more free to customize the area.
Though I know why they programmed it the way they did, so everyone could have a pond to catch the hand full of fish in them, but maybe in the Switch version things will be different!!