Why are VAL, MET and ALA substitutions commonly used for protein behaviour and function studies?
Substituting a single amino acid and checking the effect this has on a protein is a method to determine what this specific amino acid does in the protein. For example, substituting an amino acid that is part of the catalytic core would almost always make the protein non-functional. 

Alanine scanning is a technique that methodically replaces amino acids in a protein with alanine. Alanine is probably the most neutral substitution, you essentially remove the amino acid sidechain. Glycine for example would be problematic because it is more flexible and can adopt secondary structurs other amino acids can't. 

If you want to find out what a specific amino acid does, you don't want to introduce any other new effects when mutating it. Depending on what exactly you're looking at, substituting other amino acids is certainly possible. Some changes to alanine might be too drastic and you might want to substitute an amino acid that is more similar to the original one. This all depends on what exactly you are looking at.