We chose GTK over QT for Linux because Unity 5.1 ships with CEF (https://en.wikipedia.org/wiki/Chromium_Embedded_Framework) as the embedded browser and CEF already pulls in a dependency on GTK).
In what way are the native GUIs better? Are they faster/more responsive or do they look better?
Which would be more work over the e.g. 1,2 and 5 year period maintaining three guis or one? (Or is QT not quite cross platform so one ends up maintaining three inferior versions anyway?)
You can just go test it yourself, go run VLC and see how "native" it feels. Its using Qt everywhere except Android.
But if you want to develop cross platform native looking software... Qt is absolutely it. Only option. And it gets better each release. Otherwise you are going the route of the Unity guys, rewriting your program for every single system.
If you want to develop cross platform native looking software, Qt most certainly is not the only option, wxWidgets is. In fact, as you yourself pointed out, Qt isn't really native, just tries to fake the native look and feel. wxWidgets actually is, as it's a thin wrapper around the native toolkits.
This is actually an annoying problem. As a linux user lack of consistency between apps is frustrating but similarly I know people that struggle with changing from mac to windows regularly.
IMHO it is a better idea when the application enforces the same UI across platforms (like QT) than the platform expecting the same UI for all programs. On top of that QT does support native look&feel.
A lot of productivity software uses Qt. If it were not using native look and feel it would piss everyone and their grams off when system level keyboard shortcuts didn't work, when menu bars weren't oriented system native, when it didn't use the system file dialog, etc. Integrating with the OS is essential to workflow unless the application literally is your entire workflow.
You last sentence tells me you have never used a QT app on a Mac, because it does not look and feel native.
I still prefer it over any other free IRC client for OSX simply because the feature set rocks.
Precisely because users (at least iOS and Mac users) do care.
Doing native is without a doubt the right call.
Besides, the whole "wasted effort because there's 2 projects that 2 similar things" is a fallacy.
As a Qt developer let me give you a big resounding no and ask you a question: Have YOU developed with Gtk in Windows?
Since most Qt apps on linux come from the KDE ecosystem, they often pull in a lot of KDE dependancies, which means a lot of extra packages lying around your system, creating clutter, which might bother some people. The relatively heavyweight nature of most Qt apps makes them less appropriate on systems that use just a window manager rather than a full desktop environment.
Sure, a lot of GTK apps pull in a bunch of GNOME dependancies, but there's also a large contingent of GTK apps from the lighter-weight XFCE world that don't.
Outside of linux, Qt has won pretty decisively, mostly because the GTK developers aren't interested in making GTK apps look good on Mac/Windows, so long as they run.
The "out of place" argument is one I commonly used by Mac and Linux users because they want everything to look native in their OS of choice and disregard dev time (to use a different window framework for each OS) and look in every other OS.
No one can win that argument to favor THEIR own OS look over another.
Qt apps are pretty reliable across platforms and are speedy to develop so that's what should be important instead of getting an impossible native look.
Although I don't actually mind as I find that once you've got one KDE app you end up installing more as they are often quite a lot better (for me) than Gnome ones - and disk space is pretty cheap these days anyway.