Let me start off by saying this is an amazing tool. Here are few suggestions for new features/improvements.
1. Most problematic to me, the number of gates is often really small (I spam generate to avoid it, but that is probably not the best way to work around it...). With smaller sized cities it is not unusual to get only one gate and incoming road. This is highly unrealistic, all towns had minimum 2 roads and more often 3 or 4. Larger cities should have 5-6 and more gates on the other side. I feel this is the most unrealistic part in the generator, if you are not feeling like changing this, maybe you could offer an option that affects this.
2. With the exception of the temple and the citadel, there is a lack of realistic rich neighbourhoods. I got few "patriciate" but I had thin roads, while they should probably be wide (you need room for the four horses chariots) and no other features than large buildings. I would suggest to use more buildings with an internal court or with a small private park surrounded by walls (a thing that could also appear in some citadels). It is also possible to have these large houses surround a park reserved to the rich (very London like). A large house with a larger private park could also be placed just outside of the city wall (that is more renaissance than middle age type building though).
3. A common type of plaza was surrounded by buildings. "Place des vosges" or "place du palais royal" in Paris still exist in this fashion (I let you google these), it was very common even though these kind of urbanized places have mostly disappeared. I think such things would be a great addition to the generator, to vary things. That could be useful in particular when several plazas are cramped together in the centre, to add variety in the city.
4. Rivers, I am sure you already though on this one. Let me stress that most cities were either on river sides or sea side, often both. I guess that could be done easily by just changing the coast into a river. Note that most medieval cities were only on one side of the river and had just a fortified bridge, making it relatively similar than the coastal cities you already have and certainly easier than having the river go in the middle of the city.
5. Finally, double/complex wall systems. The latter could probably be done by generating a town and then generate a larger city around. either as an extension on one side only or all around. That would be both realistic and very nice, we can imagine some part of the old wall gone while other remain for even more "history" to the city.
In any case, I hope you will reserve us many new surprises with this great tool!