Ask Pokémon about their comfort levels, check their preferences in the Pokédex, then improve their habitats to increase the environment level.
Check the Environment Level
Use the PC in front of any Pokémon Center and press - to check the environment level.
Create Habitats for Pokémon with No Home
If there are any Pokémon that have no home, focus on creating a habitat for them (check the Pokédex to see the habitats they can live in), or if you don't know what habitats they want to live in, you can get building kits from the PC shop, or you can use blocks to create a building with four walls. Put at least three pieces of furniture in the building. Then have the Pokémon follow you to the habitat or building you created for them, and when they are near, talk to them and ask if they want to move in.
Improve the Comfort Levels of Unhappy Pokémon
Starting at the bottom of the list of Pokémon in the Environment Level window, talk to unhappy Pokémon and ask about their comfort level. They will tell you something that they want.
Give Requested Food to Pokémon
If they want food, you can talk to them and say "Look at this", then choose food from your bag to feed them. If they don't ask for a specific flavor, you can look at their Pokédex entry to find out what flavor they like. See the List of Flavors to find out which foods have which flavors.
Add Requested Furniture to Pokémon Habitats
If they want furniture, you can go to their habitat, and if you're not sure of the boundaries of their habitat, you can press the right control stick like a button to display the boundary.
To choose a good piece of furniture, be sure to pay attention to what the Pokémon says in their request. They will tell you a category, such as toy, decoration, or relaxation. They might also say a specific type. If not, you can check their Pokédex entry to see what types of things they like. Place the requested furniture within the boundary of their habitat, then talk to them and let them know you got what they wanted.
How to Provide the Pokémon's Ideal Habitat
An unhappy Pokémon may say they want their habitat to change. For example, they might want it to be brighter or darker, more humid or more dry, or warmer or cooler.
How to Make it Brighter or Darker
If a Pokémon wants it brighter, you can put lights around their habitat, such as Mushroom Lamps, which don't require electricity. If a Pokémon wants it darker, you might want to build a building for them that contains no lights, or you could create a compatible habitat in a cave.
How to Make it Humid or Dry
If a Pokémon wants it more humid, you could build a building or habitat near water, and make sure to water any dry grass in their habitat. If a Pokémon wants it more dry, you could move them into a building or habitat surrounded by rocks or dry grass blocks instead of watered grass blocks.
How to Make it Warmer or Cooler
Pokémon who prefer warm habitats could be moved into volcanic caves, or you could put lava next to their habitat, or you could put campfires in their habitat. Pokémon who prefer cool habitats shouldn't be near lava or fire. You can also find ice blocks in Palette Town.