did they ever fix the problem with not being able to do more advanced shipping routes making the micro management a real ass pain?
I'm not sure what it was before, but unless I'm missing something the shipping is fairly basic and missing intelligence in deciding whether to load a given resource.
Ex: Let's say you are shipping between two islands, a residential island and an industrial island. The residential island sends out iron ore and receives steel bars from the industrial island. You have one route to move those two goods. If for whatever reason the residential island fills up on steel bars, your ships will pick it up from industrial island and never deliver it to residential island, so they never pick up the iron ore from residential island.
You can mitigate this by asking your ships to dump cargo that the island doesn't need to guarantee your shipments go through, but this prevents your warehouses from getting full. When you have a lot of islands I find it most reliable to use "warehouse full" notifications to inform me to scale back resource production, which saves money and frees up labor.
You can mitigate the above problem by having linked resources in a given column such that if residential island is full on steel bars, then your industrial island is probably full on iron ore so it doesn't matter that your supply line is fucked. This will cock block other byproducts though, so it's rarely useful.
So, I stick to basic shipping routes for most things. One type of good per column, no double dipping on shipments.