Architectural themes would be nice. Rather than have everyone looking identical, you could have a list of four or so different themes to apply to a faction which would alter the appearance of buildings. So for example a Classical theme which has a lot of columns, statues etc, or a Desert theme which has minarets, arches and a general Arabic flavour.
Adaptable buildings would be nice too. Ditch the four tile housing improvements for example, and just have a single "Residential area" generic improvement. When built, you then get something appropriate to the city - based on say the main resource production. So for your food producing cities you get Estates, while industrial cities get Slums and prestige producing cities get Manors. This could be extended to certain key buildings like the town centre, town hall and similar. As a bonus, it also means you can see what kind of a city it is simply by looking at the building styles.