You all raise good points. I know quite well the frustration of seeing several people with the same name, right age, etc., and I'm yelling at the computer "which one of you had the six kids????".
For now, I'm going to split the difference. I am working through my GEDcompare, a task that I hope to finish before the next millenium rolls around, and so I am going to Profile all children of people in my direct line, issue or not. For the other children of the direct line people, I will profile them and note their children in the biography section, and keep all my notes, so that when I'm done with the GEDcompare, I can go back and give that second group of children their own Profiles (one of those not direct people had 11 children, and another one 17 with 3 wives, so it's not going to be a small job).. Perhaps someone else will Profile those children in the meantime.
In any event, the issueless offspring are not being ignored; they are just not Profiled yet. That is the best balancing act I have for now.