The storyline. I could frgive the bad gameplay if the story-line was any good. I for one think...
Follow after your deserting father who has left the safe confines of the vault to build what is basically a giant water filter. For some reason the super mutants are trying to stop him, the enlcave want to use it to kill mutant, the BoS also want to kill mutants (but for some reason don't like the enclave, despite sharing similar goals).