I've had a look at the loot but am yet to actually play the quest myself (Having trouble getting Lammannia to work).
Before even playing it though I can say safely say this; make everything harder, I've read/talked to a number of people and what I'm gathering is that the quest isn't all that difficult but has the basic mechanics to be very interesting, just make it harder.
Make players complete every section of the quest to complete it.
Boost loot so that the melee weapons fully upgraded are the best BOSS dps in the game. (Leave Mortal fears monopoly on trash dps as it is)
As I understand it there is a mushrooms upgrading weapons mechanic, similar in essence to Thunderforged, if you limit ingredient drops as follows ToEE will have good replay value and give players a reason to do EE; t3 ingredients should drop on EE only, t2 on EE and EH t1 on EE, EH and EN. This way players will have a proper reason to do Epic Elite.
Finally, as the title of the thread suggests, make it a raid, if you implement the things above properly and make the quest sufficiently challenging it should end up being an enjoyable raid that will get some solid replaying. Currently there are only 3 end game raids, Mark of Death, Temple of the Deathwyrm and Fire on Thunderpeaks, to support proper end game play we need at least 8 relevant and difficult end game raids, why not make ToEE one of them?