Omni fragments would be great for those really rare fragments, or even the ability to trade fragments you don't want for Omni fragments.
Also crafting Omni fragments in to an omni card that can be use as a wild card for evolution. Not a terrible idea either.
I do not think it should be easy to get them however it would be a good to reintroduce them now that there is such a large variety of fragment types.
When you originally got rid of them 5 star cards did not exist yet, you only had one server, and fragment variety was low. Things have changed considerably since then and I'm sure you can find a way to ration them so as to keep a balance in the game and prevent players from being able to make rare cards too easily.