The real value comes from things like DockerHub, and getting people to buy into the whole ecosystem.
And to be fair, I suspect the Docker folks were thinking less about clustering and orchestration so much as: (1) clustering and orchestration still sucks; (2) people want as good of an experience using docker as they do when spanning across multiple nodes; (3) let's make clustering and orchestration less sucky and use the 'Docker Way'[1]
[1] 'Docker Way' is a pointer to the fuzzy, difficult-to-verbalize thing that Docker enables, namely in packaging.
I don't see that changing until we get proper single-system imaging, location transparency, process and IPC migration, process checkpointing and RPC-based servers for representing network and local resources as objects (be they file-based or other) in our mainstream systems.
These things only really caught on in the HPC and scientific computing spaces, where you've had distributed task managers and workload balancers like HTCondor and MOSIX for decades. They've also been research interests in systems like Amoeba and Sprite, but sans that, not much.
The likes of Mesos, the Mesosphere ecosystem with Marathon and Chronos, and Docker Swarm bring only the primitive parts of the whole picture. Some other stuff they can half-ass by (ab)using file system features like subvolumes, but overall I don't see them improving on all the suck.
It seems the mainstream server industry has moved to more isolation rather than more interconnectedness, which is probably better for most public-facing systems.
(1) Open standards (and I'm hearing things moving in that direction)
(2) Content-addressability, so that images can be stored on IPFS.
There's a project put out by Chef (formerly Opscode) called Omnibus. It allows you to build a monolithic the package, complete with all the library dependencies and such. Chef Server is distributed with that monolithic omnibus. What had happened was that various library dependencies would cause problems with the various systems that needed to come together. It was easier to specify the precise version of the components needed. (But it also put the onus of security fixes on Chef).
That is the real problem that Docker solves. Packaging. It enables a kind of shift in thinking that's difficult to put into words. People say "light-weight containers' or whatever, but none of that really nails the conceptual shift that Docker enables. In about five years, it'll become obvious the way 'cloud' is obvious now, and non-obvious back in 2005.
You say that Docker solves this problem, but it doesn't really. Sure, it creates isolated runtime environments that avoid the clashes you described, but it only further obscures the problem of system-wide deduplication of dependencies. The real solution here is better package managers, such as GNU Guix, that can easily handle multiple programs on the same machine that require different versions of the same dependencies whilst also deduplicating common files system-wide. Once such a foundation is in place, a container system no longer needs to deal with disk images, it can just bind-mount the needed software builds from the host into the container thereby deduplicating files across all containers, too.
Omnibus and Docker are papering over problems, not solving them.
It's actually a good thing that we have these duplicates from a packaging perspective, because you completely remove the host requirements altogether, and can focus on what an app needs, and if you want to take advantage of deduplication (on disk, or in memory), then you can let another subsystem resolve that for you.
To resolve the patching something system-wide, you simply use a common base image, it's orthogonal to containers. Just because you can have different versions of a dependency, doesn't mean you need to. The main advantage of the container having it's own version is that you can independently upgrade components without worrying that a change will effect another application.
You might argue that this is a security concern, but I'd argue that it's more secure to have an easily updatable application than an easy way to update a particular library across all applications. In the latter case, we already know what happens, people don't update the library nearly as often as they should, because it could break other applications which might rely on that particular version. At least in the first case we can upgrade with confidence, meaning we actually do the upgrades.