Current gene modification mechanic is very under powered IMO. The cost to add a trait to your whole pop is too high and almost never worth it, so I only use it to mod my pop to fit new planet type. I think a good way is like the messenger event, player spend some time to develop a gene medicine, then all selected species will slowly accept and use it to get new traits (depends on the size of your empire it can take like 5 ~ 20 years for every pop to use that medicine).
And player can pay some extra influence to make a "forced modification" to a single planet, so the pop on that planet will be forced to take that modification (like the current mechanic) By this way only pop on the selected planet will be changed.
And player can pay some extra influence to make a "forced modification" to a single planet, so the pop on that planet will be forced to take that modification (like the current mechanic) By this way only pop on the selected planet will be changed.