First, I should remind to people that Linux based systems are not the only free software unix out there. The various BSD are alive and kicking, and maybe they would be more what you want than some linux distributions. That's also the freedom of free software.
Now, for the point you make "initramfs should not customizable" is rather wrong. One, you cannot prevent people from messing with it, this is free software. Two, most people do not have to mess or do not know how to do, because most of the time ( and at least for me ), it simply work.
Now, gconf backend was just file based, editable with any editor. Maybe you speak of dconf, and even in this case, there is less complexity than with registry. Microsoft switched to a more featureful system to be able to offers stuff like audit, permissions and stuff like that. While there is maybe othes ways to achieve this, having a opaque storage and forcing to use a API was not more horrible than what a SGBD do. Most problem comes from usage of pseudo-uuid, and the constant need to tweak the internal to change something.
For dbus, i can perfectly run most program as other user. Maybe you mean "I cannot run some graphical program that requires to access to shared service and some kind of IPC for that", in which case this is correct, but I would ask how you would design the system differently. If there is the concept of session, something need to start the session, and in this case, this is dbus-launch.
Network manager is working without gui, there is cnetwork-manager thanks to dbus. And network-manager is not really mandatory, you can always do stuff by hand. Of course, that's annoying for wifi, but for a server, this work fine, setup once and that's all.
Video driver in kernel space is agan rather unavoidable. If you want the kernel to manage the graphical card ( and if you want to have a text console, it has to be done by the kernel ), then you need to have part of the driver in kernel. That's what kms is about. But maybe you would prefer to have no console, or weird lock and problem because both X and the kernel use the same memory without talking to each others.
Gnome 3 is rather controversial yes, but you may notice that there is also lots of others desktop environment and choice if it doesn't please you. I found that most of the reasons listed on gnome.org to be valid, and I can understand that despites being reported twice, gnome-shell can still be improved based on various feedbacks.
Finally, you seems to not like pulseaudio, and either you have issues with it ( and maybe that's not pulseaudio ), or maybe you think there is no use to the feature ( like saner mixer defaults ). It is hard to answer without you being more specific, but if you didn't liked having video driver in the kernel, you surely would prefer to have all the features of pulseaudio ( per application mixer, bluetooth support, streaming support, ease of use to change sound output for video card with hdmi output, music being stopped when you get a soft-phone call ), being out of the kernel ( and alsa ) as well. Maybe you don't care about the features, but I am rather happy to have my hardware working ( bluetooth ).
So if you do not want any changes and if your system worked fine, you can simply not upgrade.