...can I ask a serious question?
What's the obsession with getting rid of the Safe Zones on the lower levels? Every suggestion that I seen of how to get the PC sticking to the starting city to participate consists of only removing the Safe Areas in some way or suffering a very horrible death after the cleaners advanced to a certain point.
For someone that wishes to promote progress, I doubt that Kayaba would seemingly punish all players for opening a new floor.
I would instead suggest something on the opposite spectrum: It would be the players themselves that would force them to move forward. There's two ways I can see this happening:
1: Kayaba starts handing out ownership of the first five cities out to the 'top' guilds. By assigning the ownership of Starting city to one of the greedier guilds, they would attempt to tax the populace to the point of starvation and sleeping out in the streets. Considering that a person can force another into a duel by moving their sleeping hand...
2: NPCs move from floor to floor with the players when a new cities are built. This doesn't seem like much at first, but if the system treats some of them as the backbone of their hometown's economy like farmers and miners, it would at least force the non-players to take quests outside the city to ensure the running of their city and, more importantly, their own safety. In a twist, the five highest floors would never require such quests.
Both will require the non-players to make at least a token amount of progress and increases the chance that they will eventually resort to attempting to try Magecraft.
Illya the Builder
When it comes to setting up the basic buildings needed to survive before a full town is established, I can see her building. After it's safe? Can't really see her sticking around...
Crafting Enhancement
I can see the reason of simplifying some of the crafting systems in the game, but I think by doing so, Kayaba's actually weakening some of the progress of magecraft. Imagine Shirou engraving runes into a sword during forging, or a player engraving others into wooden planks before Illya uses them to build a guard tower.
By making the crafting process more complicated and realistic, he's giving the players more chances to experiment and discover newer ways of using magecraft with mundane crafting.
Church
Instead of having it as a set of cities where the church rules, why not have it as a set of dungeons in the game to get the players use to fighting members of the church in the real world?