>is out of date when no less than 4 times that I installed software I had to fire up alacarte to add it.
Alright, I'm curious... what software and what DE? The XDG spec defines a standard place to look for these files, and it's honored by KDE3, KDE4, Gnome2, Gnome3, MATE, Cinnamon, Budgie, ... and probably more that I'm forgetting.
So, if it's not happening, it's either a bug on the software for flat out not shipping it, or a packaging bug on the distribution's part for not placing in the correct place. But like I said, I've not encountered this in the wild for longer than I can remember.
>And the shell problem is just me describing a situation exactly as it happened, chsh would not change the terminal that Gnome Terminal used, I had to manually change another setting.
:/ I just tried it on a 16.04 install and on an Arch Linux install it worked as expected. Gnome-terminal defaults to "Run my shell" but has options to override it which are not on by default. You can see here where it uses your user set shell: http://bazaar.launchpad.net/~vcs-imports/gnome-terminal/mast...
>With Linux I get "Well I don't know what you're doing wrong because X has worked for me just fine".
From my experience, most times when I sit down with a user, and walk through troubleshooting, I see things, ask and hear back "Oh right, I forgot I tried fiddling with that too, did that make it worse, oops!".
If these things are so easily repro'd, there are people who would love to have bug reports for them. I've filed a couple GNOME bugs before, it was a straightforward experience.