The FFXI merit system was excellent. It was a timesink that didn't feel like one because you were making tangible progress with foreseeable goals that don't rely on RNG, ie. "If I gain 100k XP, I know I can increase a stat of my choosing PERMANENTLY by 1". Not only does it reward "hardcore" players for their efforts without overpowering them (you would set a cap for each stat of course), but helps reduce the complaints stemming from skipping mobs in speed runs, as well as atma/alex farming. This brings new light to SE's idea of keeping veteran players involved in old content to help out the new players (without pissing anyone off).

This should be easy to implement as well, just take a look at the upgrade system for Atma>Animus weapons, as well as the "Bonus Attributes" in the "Profile" tab for your character and the rest practically writes itself.

I like the OP's idea also, I just think more tokens and such are unnecessary.