IMO the problem is not the lack of this "so-called" city center effect, but rather the lack of height variety in the game's skyscrapers.
In Singapore where I live, all the buildings are almost the same height.
In this photo, you can see public housing estates (like "commie blocks") built in the 80s at the front, the newly built public housing complex called The Pinnacle with sky bridges connecting the blocks (sort of primitive MegaTowers) in the middle, and the downtown core area at the back:
Yet there is still a distinctive skyline when seen from the other side:
...due to factors such as the CBD being at the edge of a bay, the low-density pre-war godowns on the riverfront (now converted to restaurants & bars), the colonial-era buildings such as the Supreme Court and the Victoria Theatre on the opposite bank, and most importantly the different heights of the skyscrapers, which interesting are mainly due to changing height limit policies over the years.
And the only reason all the commercial buildings are at the same place is because they are only allowed to grow there.
Just for fun, here's city planning in real life - a land use plan for 2030 with different colours for different zones just like in the game (anyone who played Just cause 2 might be familiar with the island names):
So yeah, I think the game's high-rise ban when combined with more buildings of much more different heights should work pretty well.