GPUs are SIMD machines, so they're executing the same instruction simultaneously on all the active cores. That means if you have code which branches, it has to mask out the cores which follow branch B while it executes branch A; then has to mask out all the cores which follow branch A while it executes branch B. In other words, if at least one core follows each side of the branch, it has to execute both branches.
If all cores branch in the same direction, you don't get that penalty. A large part of optimising for the GPU comes down to arranging your data and code so that this can happen.
GPUs suck at any problem that cannot be easily divided. If you can map a function over arbitrary chunks of self-contained data GPUs will perform better.
If all cores branch in the same direction, you don't get that penalty. A large part of optimising for the GPU comes down to arranging your data and code so that this can happen.