Usually, when I have to deal with these crazy complicated YAML files at work, I'm not thinking, "I wish they had just turned all the configuration into a mess of shell scripts." I'm thinking, "We really need to clean this up. It's way more complicated than is necessary."
You have a point. A mess of shell scripts doesn't really sound like an improvement. If the config is too complex and the config consumer can be changed to simplify things then that should be the way to go.
However, if the config is a travisCI YAML file that is really just a glorified list of commands I don't think bash or a makefile is a bad solution. Take as much as possible out of the CI config and use a neutral standard format like a makefile to encapsulate much of your logic.
Then when TravisCI stops offering free usage for open source, its easy to move, because your format isn't specific to a vendor.
