For me the ideal layout is so, so dependent on how I plan for the town to be. I like to come up with a theme for how the town will be decorated and landscaped, and I may have a few ideas already for areas I want to have or emphasize. So the town map and certain features have to gel with what I have in mind, and what would be perfect for one town may be not-so-good for another town.
For my town Citalune I wanted the top half to be fairytale-city themed, so that side of town had to have the town hall, train station (both fairytale), and Re-Tail fairly close together to help achieve that city-like feel in the top half. But I wanted the bottom half more natural, so the town tree had to be on that side. In one of my other towns, Lorien, I wanted the town hall directly centered above the town tree to create a unique area connecting them both, several ponds grouped together in one part of the map for the location of a bathhouse, and pears (so that they would be gold to match the October golden foliage). Having just one pond in a structured city-like town may be best, but in a forest-like town having many ponds may add a lot to the atmosphere. So you can see how I don't apply the same criteria to every town.
It's really interesting to see what people find essential or important for town layouts in general, though ^_^ I agree that rocks are important to comb through and see if there are any in truly awful places. I think another dealbreaker is if I cannot find a decisively good place to put the mayor's house, like maybe there's a perfect spot for it, but it's taken up by villager houses. :/ Often the fruit is fairly important to me, but I may shoot for different fruit depending on the town theme. There are certain river shapes that have a certain
je ne sais quoi appeal, or vice-versa.