I had the same problem in my first omega cities, but following this logic made my cities almost 100% omega. First, how it works: the omega factories deliver drones to residential, and omega to industrial, and the industrial factories are the ones that deliver omega to commercial. So, if your factories don't receive enaugh omega, your commercial won't.
So, what are the reasons omega factories won't produce omega enaugh? 1. Omega factories are not getting enaugh workers (traffic or population issue). 2. Workers are ill (happens a lot in industrial areas). 3. Omega delivery trucks stuck in traffic (each omega factory has limited trucks, 4 I think, so if they have to travel much distance to deliver, then they won't get back in time for the next recharge, so the factory will stop producing until it has been emptied and has more room to store it. The same applies to the drones).
How do you know when to add a drone line or a omega line? So, I usually look if industrial is 100% omega (and if you hace enaugh I, then your C will become 100%), and if that's the case, I place drone lines until residential is 100%. I don't know how many factories are optimal, but with 3 I could support over 200k population.
I also discovered that once the VTOLs are up and running, trade depots are pretty useless for omega cities.
Now, looking at your city screenshots, from what I can see, I'm almost sure it's a traffic issue. It seems like the border straights are too long, and the trucks have to travel a lot to deliver the omega. Try placing an omega factoy in the opposite side of town, and making a bit more road conexions in the left side (I'm talking about the omega map screenshot).
Good luck!