Popularity - Popularity points are cumulatively used to determine your inn's popularity. The more total popularity you have, the greater the number of guests that will visit your inn regularly.
Scenery - Scenery directly affects the amount of satisfaction points a guest gets from using the facility. Decorative objects provide different amounts of scenery points, and facilities directly next to natural decorations receive more scenery points than facilities places further from the decorations.
Layouts - Utilizing layouts allow you to maximize the number of facilities that receive bonuses from placing units within 3 tiles of each other. Layouts can be used to increase price, popularity and scenery in facilities.
An example of a layout with many combos that boost the popularity,
price and appeal of each facility: http://3.bp.blogspot.com/-yTmLyuI0jAM/UASABejnHnI/AAAAAAAAApY/wNVZ31eqTVI/s1600/IMG_8669.png
This site walks you through some of the reasoning for certain layouts, explains why things go where, and nicely demonstrates how using shop/facility/combos affect the game / future games.