It would be nice if lower level instances could be changed to reflect the average gear score in the party.
For example, the average gear score is 2000: Bethomia bosses have 1.800.000.000 HP or something instead of their usual 90.000.000 ish along with other increased stats (atk, def, ..).
I think the custom implemented 'gear score' attribute almost asks for a change like this, and I think taking the average of the party as a starting point should work just fine.
Perhaps a new difficulty mode could be implemented as well:
- easy (original)
- normal (original)
- hard (original)
- "According to gear score" (new)
That way the original instance difficulties can still be played.
The "According to gear"-difficulty's rewards could also go according to average gear score, e.g 1400-1600 = tikal level rewards, 1601-1800 = inferno level, 1801-2000 = gorge level, 2001-2200 = rofl level, ...
This might be a lot of work initially, but I urge you to think about this 
this way you don't have to implement/rework entire instances anymore and should just be able to alter mob/boss attributes according to a dynamic value.
EDIT 1:
About rewards, instead of dropping actual gear perhaps Proof of Myths could be dropped instead (more or less according to gear score), and those stats (tikal,inferno,gorge,rofl,dark core) could be pulled from those instead.
Given the respawn time on worldbosses, this would be incentive for people to just run the instance they want and still get rewards for it.
People would then still need to run the custom instances to get gear/cores/...
