Some of these things are related, particularly Gnome 3.
Leaving aside technical considerations, Gnome's development (under the umbrella of Freedesktop.org) adopted a distinctly authoritarian tone; you will have your desktop this way, it will use this init system etc. The deliberate coupling (logind for Gnome3, see also the above poster's example of pam_systemd for similar) was not accidental (Poettering has said as much) and the resulting controversy was therefore not surprising.
I think - and I'm pretty sure it's been said elsewhere - that had systemd truly stayed within scope and looked after pid1 only, we would not be having this discussion. Instead it also became a userland hydra; that's the rub.