The issue it seems right now, is they assume everyone is going to pick the same few "general skills, and there won't be any differentiation between people or subsequent runs.
The true solution to this is to make the other perks more desirable imo. For one, I think combining multiple things into one perk was a bad idea. Give lots of options, compile a list of what people aren't taking, and make sure there is a good reason to take it, or replace it with something else. Don't artificially force us to play a pre built set of classes with a difficult way around the limitations, at least not when we had so much freedom previously.