You should always consider that resources are also of global value, and are not mainly ways to randomly improve the output of certain city sites. Also, the usual player doesn't want tight city packing (it's quite annoying unless you're obsessed about having every historical city), and you can't even avoid that when you flip them.
Europe has tons of packed cities, heck France, England, Spain, Portugal are ONLY packed cities, so why not include Damascus, which was the most important city in the Middle East up until 750, and then again under the Zengids/Saladin. A great thing you could do with Damascus, is if you have the Egyptians respawn as the Ayyubids, you can have Damascus flip to them, along with Egypt, wouldn't that be cool? And if you noticed, I'm doing very little packing, in fact adding Damascus, and moving Antioch and Ikonion as I stated, while adding one wheat and one fish, would be fine for the region. Plus having Damascus as a capital, would stop the Byzantines from overrunning the Levant EVERY single time. I think you should try it, like I have in the past, before coming up with such assumptions.
I also don't understand what's so "annoying" about the stone underneath Baghdad?
Are you kidding me? Of course its annoying, it should be next to it! Plus there is already one stone to the West of Baghdad, so why do you need another one underneath? What purpose does it serve, other than making it look ugly? Its not only me, don't you hate to build cities on resources?
Where? In the Levant? I can't see why it warrants such a treatment, it's not a particularly fertile area.
Thats where you are wrong Leoreth, right up until the Timurid invasions in 1400 or some scholars say 1600 under the Ottomans, the Middle East (the Fertile Crescent) was very fertile. It was later that desertification began, due to soil erosion. Otherwise the Levant hosted some of the most important cities, along with Damascus which at its prime was huge, not to mention it hosts the fourth holiest site in Islam.
Currently the Silk Road company is under used, and I know thats because its still being tested. What should happen ideally is that a couple cities in China start with the Silk Road, and it spreads westward, city by city, and whenever it reaches a city it gets a commerce boost. Certain cities should also get an increased chance of attracting the Silk Road like Samarkand, Damascus and Constantinople.