OK so the Sub Project Mega Milestones are kind of nice but don't appear to contribute to anything else (like Maxwells or MiRBs), fair enough, but how about throwing those who bother to take note of the Sub-Project MegaMilestones a bone and give a separate badge for them. Perhaps you could just stick a big S in the background of the current MM and otherwise keep it the same, colours and all.
Just a thought.