Of course, I can understand that if you prefer living in a much bigger city, you might not like it in Mainz. Ultimately, you should be aware that it's not exactly the biggest city before you move here. (But you are pretty well connected. By train you can be in Berlin or Paris in 5 hours and in Frankfurt in half an hour, which is also home to Germany's largest airport).

However, I cannot understand some points:

Public transport is okay if you ever manage to figure out which bus is going where.

It's not that difficult. I don't find it any more complicated in Mainz than in other cities. For some time now, the information for the buses has also been integrated into Google Maps, so it really couldn't be much easier.

The organisation of the uni itself is a catastrophe at least for my subject, and it is only getting worse. We went from 4 different programs for our timetable to 5 last year, and still nothing is ever correct.

This has more to do with the organization of your field of study than with the city. (And I don't understand what you mean about the 5 programs for the timetable. Do you mean Jogustine? What are the other four? Why not just use your own calendar app of choice?)

Most shops are generic, and there is no real mall or something similiar. Not bad in general, but sometimes I don’t want to walk around the whole Innenstadt to get everything I need.

As if there would be non-generic shops in a mall. I would say the city centre is small enough to get all the things you need by foot.