Here's the thing folks... Apple does not sell OS X as a "flavor" of Unix, it only says it's built on top of it. They can modify it any way they wish.
OS X != Unix. If you want rootless, GO USE UNIX.
I think you (and some other people) are fundamentally confused in regards to this. Being UNIX does not mean that you can change everything, it merely means that your OS is built around a certain set of well-defined abstractions and behaviours. I think because of popularity of Linux systems, which like to advertise themselves as being infinitely configurable (which is quite funny in itself), people have this particular view of what a unix system should be. However, UNIX is not Linux and Linux is not necessarily UNIX. OS X however, is UNIX, because it is build around one of the few proper UNIX implementations (FreeBSD).
In the end, it is the matter of picking the right tool. Need to modify the base system, recompile the kernel, do all kind of low-level wizardry? OS X is not for you — use a suitable Linux distro. OS X is built around standardised behaviour and it enforces this behaviour both on the developer and the user. This is a good thing(tm), because it makes software behave in a predictable way.
Why should anyone have to use all these workarounds just to get their computer to work properly? The mere fact that any of this is necessary says a lot about where Apple is headed - and it's not pretty ... And even with it on, I find it hard to believe that it really stops anything but functionality of the machine.
You won't even notice that SIP is activated unless you are using software that is badly written, software that hacks system components or software that violates OS X development guidelines. Simple as that. And SIP does not prevent any noteworthy functionality, unless by functionality you mean "its my computer, so I am entitled to modifying anything I want". As I have said before, if that is your argument, then OS X is simply not for you and never has been.
I for one, don't see the benefit of a few extra features as a worthwhile trade-off for all the problems SIP is causing. It seems that trying to wall off a major part of the OS is a very bad idea. As for it being a "security" feature, that's a joke. Sounds like a lot of people are turning it off.
SIP is not causing any problems, badly written and outdated software is. It does not wall off a major part of the OS, it isolates the core system from the third party, user-managed tools. Which is btw the fundamental design of UNIX systems and the traditional role of the root user. Unfortunately, nowadays the root user is often abused, which makes more strict security measures necessary. And the truth is: Apple is right. There is absolutely reason for anyone to write to most locations protected by SIP*, unless you want to change the core behaviour of the OS (i.e. — hack it). The only people who are really hurt by SIPs are hackers (used here in two ways — both people who want to hack your computer and people that want to hack their own computer). Yeah, some programs might have issues because of the lazy coding. This will be fixed in time. Apple is big enough to enforce it. And better written software = happier user.
Finally, minor complaints on the forums does not mean that a lot of people are turning it off
*An orthogonal issue is of course whether SIP protects all the relevant locations and whether all locations protected by SIP are relevant. It can be that it also locks out some stuff that should remain accessible. However, I have been using 10.11 since early summer, I work almost exclusively with UNIX-based tools and UNIX development, databases, a lot of in-house developed software etc. and as said before, I never even noticed that SIP was there.