Disclaimer no experience with vaccine development but...
Two problems with some types of engineered vaccines. The first is people can have existing immunity to some component of the vaccine. And the immune system wipes out the vaccine before it has a chance to generate strong immunity. Second people develop immunity to proteins in the vaccine that aren't present in pathogen you're trying to vaccinate against.
As an example I think one of the vaccines based on modified viruses uses a different virus in the first and second shot.
Two problems with some types of engineered vaccines. The first is people can have existing immunity to some component of the vaccine. And the immune system wipes out the vaccine before it has a chance to generate strong immunity. Second people develop immunity to proteins in the vaccine that aren't present in pathogen you're trying to vaccinate against.
As an example I think one of the vaccines based on modified viruses uses a different virus in the first and second shot.