I completely agree that it's a mess to have all the comments for related tickets displayed in all the tickets. We should be able to independently manage tickets even when they're related.
I just ran into the same type of issue when creating a follow-up for one of the tickets that is in a "related" relationship with another ticket. Some thoughts I had would be to provide a note in the comment (follow-up or other type of comment) indicating the ticket in which the comment was made, and then providing a link to the other ticket. This way, their relationship is maintained but they're managed individually.

Thanks for bringing this up. We'll discuss it internally and see what we can come up with as a solution.

Changed from a Problem to an Idea and marked as completed. This change will be in the next release. Now, tickets will retain their comments -- they're not all aggregated to the primary ticket.