Regarding the many different Linux configurations, then I agree with you in principle. But I don't think the fragmentation of Linux has been really helpful either. It is clear that there now is a major push to reduce Linux fragmentation.
I think the "every distro is a separate island" doing everything their own particular way, is something that will disappear. But perhaps that isn't so bad, maybe the interesting thing about different distros, aren't that they all place their shared libs in different subdirs, but rather, what software platform they deliver above the system level. Less Linux fragmentation will definitely make it easier for distro maintainers and upstream developers in many respects, so perhaps this will release energy to do more cool things, instead of patching up differences. I mean, a pure systemd version of Gentoo will still be Gentoo, it will just share some basic OS characteristics with other Linux distros that will make it easier for upstream projects to support it.
I still think there will be many, many different Linux distros in the future, catering for either the mass market, or specialist use, I just think they will be less fragmented and different at the core system level, thanks to systemd etc.
I can see the value in that. At some point I expect I'll set up a box with a mainstream distribution if only to run Steam, for instance. The current fragmentation does make it difficult to run software packages that make assumptions about how the system is laid out. I can often get something working, but it can be a pain.
If I had to choose between very fragmented or completely uniform, however, I'd choose fragmented. We can't predict where Linux will be used in the future, and so we may need the core-level diversity that fragmentation brings. It's about more than just where libraries are placed, but about ways of doing things. Being able to drop in an alternative system-level structure lets us try out new principles, such as systemd versus sysvinit for instance. We might all be using systemd in 10 years, but I would bet you nobody will be in 50, so if we're no longer able to experiment with alternatives because we're locked into one system, that new alternative will come from outside the Linux ecosystem. It's evolution: stop growing and settle into a niche, and eventually something nimbler will outcompete you.
This is a similar discussion I have with the rest of my family: they use OS X because they see a computer as a tool to run software, whereas I also see it as a testbed to experiment with the running-of-software as well. I value diversity and flexibility over ease of use, which is why I've stuck with Slackware and similar distributions, and only occasionally use a package manager. That's an issue of taste, however, and as they say: de gustibus non est disputandum. I know I'm in the minority here, but I'm hoping the majority doesn't abandon us as it feels like is happening at the moment.
I think the only way the smaller distros will have a say in the new direction Linux is taking at the moment, is to organize and counter it with their own proposals.
Yeah... There are some interesting alternatives out there for various parts of systemd - I've been using runit as init system for a few months and like it - but few of those are gaining enough traction.