@Gladiola, I am a bit busy nowadays with RL matters. I spent some time with your city, but honestly I don't think it is possible to incorporate all the changes you want--it is simply much beyond what you can do with 25 expansions. Also, you should know that you are already familiar with the key principles of city planning, so any improvement from your design will at most be minor (e.g., a couple of tiles from fewer streets).
This is the outcome of my work. This is not complete, because I cannot find ways to get enough pop and culture. A few notable changes I made are as follows:
1. I upgraded workshops to Lv15, as lower-level workshops are less efficient.
2. To do so, I needed to expand the usable spaces "horizontally." Therefore, I moved cultural buildings located on the right-hand side of your layout to the bottom of the city.
3. I upgraded one Elixir manufactory to Lv15.
4. I needed to replace some pure-culture buildings with culture-pop hybrids to get more pop.
I think my city design is quite close to what might be optimal (I saved 3 more street tiles compared to your design). Also, I like my design because it looks quite organized. However, I still couldn't have enough pop and culture, and I also couldn't fit one marble manufactory. The culture problem might be resolved if you upgrade all the streets, and the pop problem also might be resolved if you add several extra levels to the GA. That being said, I still haven't incorporated other changes you wanted--one more crystal manufactory, more levels on the main hall and the barracks. To me, it seems they just cannot be all fit in a city of this size.
If you are interested, you can take a look at my city. I have recently entered Chapter 6, but I haven't built any guest-race buildings yet, and the size of my city-27 expansions--is similar to yours (I recently purchased 3 expansions, but I am not using them yet). If you compare the two cities, the biggest difference is the number of residences. I have replaced many residences with culture-pop hybrids as well as evolving buildings from events. In addition, I need fewer population in the first place because I have fewer manufactories (for example, I haven't built any T3 manufactories because I am currently producing excess T1 and T2 from my city, which then I can trade with T3). Lastly, I intentionally did not max the level of my manufactories because I realized that higher-level manufactories require too much population. They are kept at Lv 12 ~ 13, and they still produce enough goods for me. Therefore, compared to upgrading them to Lv 15, keeping them at Lv 12 ~ 13 allows me to save some space for pop.
The bottom line is that you have to think about whether you really need all those manufactories and other buildings/building levels. You can probably get by with fewer/lower-level manufactories, which will open up more spaces for anything else that you want to add to your city.