Separate /usr is extremely common, and this isn't going to go away anytime soon. It will also never be possible to make the transition automatic: it could well require repartitioning in order to get a big enough root partition, or LV resizing etc. So having a unified / and /usr will only be possible to do on a fresh install. Initially, it will just be an option, and it won't be the default. But it will be /possible/.
Having a unified / and /usr isn't a new concept. Debian GNU/Hurd was doing this for years, with a /usr -> / symlink. It won't take much work to get this working on GNU/Linux. The main thing is finding and eliminating duplicate paths which would be overwritten; most of the duplicates are workarounds due to the split in the first place.
It's very common for people to have a knee-jerk negative reaction to this: after all, it's a radical departure from what we've been used to for decades. However, please do take the time to consider what you have gained from a separate /usr. For the vast majority of cases, nothing is gained other than needless complexity.
Most of the historical reasons for having the split are long gone. Sharing /usr between machines makes zero sense when you are using a modern package manager. Having a separate /usr for booting no longer matters now we have a capable initramfs which sets up the system sufficiently to allow any filesystem to be mounted: we can just mount / containing /usr directly; previously it was not always possible to do this if you needed to e.g. start up RAID arrays, discover LVM volume groups, bring up networking etc. Previously, you needed to do this using programs on the root filesystem as part of the startup sequence. Today, the initramfs does all of this. Now we have /run [I implemented this for Debian over the last two days in base-files and initscripts; should be available very soon] we are looking much nearer having a read-only / by default. It's common to have a read-only /usr; now you'll be able to have a read-only / *including* /usr.
Regarding top-level namespace pollution, most of the directories are duplicates, and those that are not still logically fit.