I'd suggest making it so that only experience from the "bonded" destiny is lost when one undergoes an Epic TR, then gains the past life feat and a number of experience points. At the very least, it would be nice to be able to skip the harbor and marketplace quests.
One of the flaws of the epic destiny system is the amount of time one has to spend getting experience in an ED that does not benefit ones' character. Now, if it's really necessary for players to lose any of those experience points, then something needs to change in the system in order to reduce the amount of grinding. Some suggestions:
1) Make it so that epic levels give caster levels for any spell-casting classes, and uncouple caster levels from ED levels.
2) Remove the ED level requirements for getting from one ED sphere to another, put in connections between spheres so that on one has to go through the martial sphere unless they want to, or get rid of the map entirely.
3) Somehow make twist of fate slots easier to aquire and/or upgrade. Perhaps you could give out fate points when leveling up instead of with ED levels?