That's true, but also irrelevant. GNOME Shell isn't an app, it's part of the infrastructure.
Rhythmbox? C.
Evolution? C. (Geary? Vala.)
Shotwell? Vala.
LibreOffice? C++.
gnome-terminal? C.
There are no GNOME apps written in JavaScript yet. The fact that they're using it in the shell is promising, but if they want app developers to pick it up en masse they need to lead by example.
Most criticism centres on the design, not the technical aspects, I think it's fair to say. It's an example of a fairly large, complex, and smooth application written in Javascript for the Gnome platform.
I am looking forward to more apps using JS to see how well it all works in practice though. More docs and support will help this I hope.
I think that the language is not necessarily so disconnected from the design as you say. Language influences thought, and can thus have a large effect on how people solve problems (ex. When's the last time you used a lightweight, snappy feeling Java app?). If Javascript leads people to designs like the GNOME shell, I'd much rather it be kept out of GNOME's toolkit.
I think it's also important to consider not only how JavaScript may influence developers while they create software, but also what its voluntary use says about the developers' experience, knowledge and judgment.
It's one thing to use JavaScript when you're doing client-side web development, where it's basically the only option, even if it's dressed up as CoffeeScript or TypeScript. But it makes absolutely no sense to voluntarily use it when C, C++, Python and even C# and Vala are available. Doing so would be a significant show of very bad judgment, in my opinion.
If you need performance or power, using C or C++ makes perfect sense. If minimizing development time and effort is important, then Python will work extremely well. Vala and C# generally fix somewhere in between. So there's absolutely no place or need for JavaScript, which is inferior in every respect. No intelligent developer should ever feel the need to choose it when developing GNOME applications, given the much superior alternatives. Anyone who does want to use it probably shouldn't be contributing to a project like GNOME in the first place.
