Okay, I couldn't wait for it and so I've produced an example of what I think should happen instead. The idea I have is that each faction may build a base to the wonder, a mini-wonder as it were, taking 90% of the production needed to make the world wonder. Each faction may build 1 of these base wonders. Then the first to upgrade it to the world wonder is the only one that can do so at only 10% of what's left over for production.
The compromise is as follows, each base does a small amount of what the actual wonder will produce. For example, the treasury vault produces 1% intrest on all your current gold... the base will only produce .1%
It is still a bonus, but not a very good bonus. Ereogs Tower is one where it is pretty good to build whether you upgrade or not... +1 mana per turn vs. +1 air shard. Obviously it is better to get the air shard (big time), but it is not that much better than the faction base one. I think this is a good comprimise and it brings in unique faction buildings as well that are not completely lost on the player.
What is left to do to finish these mods, is mild redesigns of lesser versions of the wonders and possibly new map icons. I hope the devs find this interesting enough to put in, if not I'll try to keep it up.
A legendary Hero's version:
https://dl.dropboxusercontent.com/u/75549875/Fallen%20Enchantress/WondersBase/WondersBaseLHv0_5.zip
A Fallen Enchantress version:
https://dl.dropboxusercontent.com/u/75549875/Fallen%20Enchantress/WondersBase/WonderBaseFEv0_5.zip