Now the posix APIs feels like the worst of both worlds.
Most applications shouldn't really store data on the filesystem, and probably not even configuration. Most applications use a database for a zillion reasons (e.g. better backup, restore, consistency, replication, transactions, avoiding random writes, ...). Yet the filesystem is also not a great interface if you're building a database: you want more control over flushing and buffering and atomic file operations. The filesystem is mainly good at storing compiled code.
The "everything is a text file" interface is not great anymore, either. Simple manipulation of the output of basic commands (like text 'ps') requires error-prone parsing and quite some skill with things like grep, sed, awk, sort, etc. That's OK for experienced sysadmins working on individual machines, but doesn't integrate very well in larger systems where you have lots of automated access to that information. I have some experience doing sysadmin-like work, but I still run into problems with simple things like spaces in filenames and getting the quoting and escaping right in a regex. One option is for it to be more database-like, but that's not the only option. Erlang provides nice programmatic access to processes and other system information while still feeling very free and ad-hoc.
Of course, Linux is still great in many ways. But it feels like some of the core posix APIs and interfaces just aren't a great fit, and a lot of the interesting stuff is happening in non-posix APIs. And applications/services are being built on higher-level abstractions that aren't tied to single machines.