In terms of "altered realities" while I apologize for not reading the whole thing, one thing that I've thought would be interesting would be to use WoE as it sounds like it should've been used.
On http://wiki.ffxiclopedia.org/wiki/WoE it describes the zone as:

"All memories and futures that are deemed "dispensable" by Atomos are devoured, digested....and deposited in this wasteland of memories and time, the world between the worlds: the Walk of Echoes. This realm beyond the Cavernous Maws contains numerous floating structures, walkways, and stairways suspended in an empty sky, with a strange, fanged wormhole situated overhead."

Instead of something that sounds interesting from what is read in the above, we were given a same type mob with bigger mob bosses battlefield fight. Upon reading the above I always though it would be interesting to implement it almost in the sense as voidwalker is now, except more story based. Basically Atomos could call on you to be a "warden" to clean the discarded memories that have manifested in his territory and taken form as the heroes of those lost dimensions. With that in mind you could find yourself face off against something like a Zeid in PLD garments wielding the Lightbringer in a dimension in which he brought destruction through the very blade he is wielding now. By subduing this altered Zeid you would obtain a KI memory which could then be redeemed for abilities, traits, spells, combat/magic skill augments, etc.

Basically WoE could be a playground in which the adventurers find themselves synchronizing with the lore of other dimensions in order to bring order to Atomos's lair. While inside the WoE you would be able to augment yourself with little limitations, outside the territory you would be limited with how much of the "Dimensional Lore" you could augment yourself with. While in a sense it does sound like abyssea, the difference in mind that instead of attribute buffs and traits you would be "buffed" with augments abilities, new traits, access to casting certain spells on another job, traits that increase magic dmg of a certain type, upgrade of combat skills, slots to place new spells learned, etc.

I dunno it's just when you look at WoE you can see it as a definite lost of potential from what it defined itself as. Where if it were just something more then a "battlefield where you face off similiar mob types" it could've been something worthy of calling an end-game zone.

I apologize if this is off topic, but judging by what you were suggesting I would think that this may be able to tie in with what you had in mind.