It seems to me that the best way to prevent fringe trait stacking that results in undesired gameplay is to implement a system where you can only have one unique trait active at a time. So if you stacked 3 Lively Spirit traits, you'd have the most powerful one (highest ilevel) active, and the other two would be inactive.
I feel this would also help distribute trait desirability and reduce the feel that there is one single BIS trait that you have to shop for, thus rendering many piece of gear worthless if they don't have that trait.
I think this would result in a more diverse trait selection and less focus on hyper-performing traits at the cost of all else.
Thoughts?