> Do you really think that's acceptable?
For the most part, yes, I do. Most of it is not in any way anything that can be legally protected. Some of it may be, but suggesting that all of that 132 page document is somehow an indictment of Samsung is misleading. They may have stepped over the line, but analysing how to adopt the best part of what a competitor does is part and parcel of competition.
But to your main question: In addition to the design: Brand, integration with the rest of the Apple ecosystem, investment in apps.
To put it another way: If it was only design, you can buy <$100 Android phones from China that are skinned to look at act like iOS, in shells that look like iPhones, at least you could the last time I checked (cheapest I've seen at AliExpress was $15). If it was only design there'd be far more than them, and they'd actually sell at decent volumes. But they don't, because they don't give people the other things they want.
> As for logistics and manufacturing integration, Apple don't even make their own phones.
I don't know what you think that suggests, but what it actually means is that Apple as part of their effort of streamlining their supply chain has largely outsourced the risks on the manufacturing side while they still place a massive amount of demands on their manufacturers that they're able to thanks to their volume.
Tim Cook's rise in Apple was largely down to closing down internal manufacturing and instead dictating terms to contract manufacturers that virtually removed Apple's inventory, and doing things that other people thought were crazy, like starting to ship electronics by air, betting it'd pay for itself by letting them not have e.g. weeks worth of inventory on ships and being able to respond to demand changes much faster (and hence needing to place orders much later). Apple's shift to using contract manufacturing was part and parcel of the company more tightly integrating their entire supply chain and shortening it drastically, by entering long term contracts with companies close to e.g. their component sources.
> How incompetent do they have to be for Apple to have that as a primary advantage for decades?
Not at all. They had $50bn worth of operating income in 2017 from Samsung Electronics compared to $61bn for Apple. Their Android business is low margin because it is extremely competitive. Their contract manufacturing and other product lines are generally much more profitable.