Doing a true custom faction in Elemental wasn't as easy as it should have been. It involved a lot of scripting and effort to put in a player designed city so your created faction could have it's own truly unique look. In Gal Civ 2, creating your own fleets with custom designed looks was easy as the ship designer was incorporated directly into the game as a choice. When designing a ship you could go with the stock default design, OR, you could design a custom ship from the ground up designing how it looks.
For FE I would LOVE to see the building designer incorporated into city building as a CHOICE if the player wanted, to design how a building looks using the building/tile creation tools from Elemental. Honestly, I haven't followed FE enough to know how it will work in FE or if it's the same from Elemental, but, during building placement or city design it would be nice to have a button in the interface that could be pressed and take you to the building/tile editor to let the player design the building on the spot. This way every created faction can have it's own unique look to it without the need for all the scripting and effort by us modders to make a faction use a city that is unique unto its-self.
This of course is a players choice. Designing a building for your faction won't change how the building works in game-play terms, only how it looks. If the player chooses to use their time to create every single building their faction uses then that's something the player can do. Not doing so would have No Effect on game-play and what your buildings do, but, it Would let players become more attached to their created faction and even let them fight against that faction later with another player created faction and have it retain the look the player created for it.
This would be far preferable to the steps that had to be taken with the Elven Mod and Undead Rising for Elemental. I don't think it would be very hard for the team from a coding perspective and shouldn't take long to do as the fundamentals are already in place. The pay off would be a game that the player could be much more invested in should the player choose to be and in the long run could add a lot to replayability as well.