My biggest issue with these apps is the inability to share memory. If I have Viber, Slack, Atom and regular Chromium open at the same time, they all consume copious amounts of memory which I assume is due to the constant overhead layout/JS engines need to keep resident per app.
If I'd somehow opened all these as tabs on Chromium, they would plug into Chromium's already-allocated shared data structures and the memory consumed would be quite lower. I can have Facebook Messenger, Deezer and Gmail open alongside 10+ other tabs at all times, but once I start Slack and Viber alongside Chromium (or Skype for Linux Alpha, or Visual Studio Code, or Black Screen, or any of these trendy hybrid-web-desktop apps), Linux starts screaming and swapping things around; as a result, everything becomes sluggish.
Also, the apps themselves feel a bit laggy even when they have all the memory they need. I know the comparison is not fair, but using, say, Code::Blocks or QtCreator (which are full-blown IDEs) with Atom, I can feel input response differences for some reason.
I have a low amount of RAM on my home PC and I plan on upgrading it, so you can say that my hardware is the problem, but clogging up memory like that is always a waste.
As a test, I just opened Popcorn Time. Right after startup, it uses 200MB of resident memory. The whole GNOME shell + the Xorg process consume around 280MB combined on my PC. That's insane. Yes, it looks beautiful, but it's nothing you can't do with Qt these days. It also supports JavaScript. QML is not hard to learn. It's available for Windows, Linux, OS X, and even mobile. Ditto for GTK+ 3: Vala is beautiful, practically C#, and good enough for at least the UI layer of your app, if not for the whole thing. Qt and GTK+ are both open source and LGPL, which means you can freely link to them even if you develop proprietary software.
I just don't see such a need to make today's apps so bloated (and I don't consider "people have enough memory nowadays" a valid argument). If it's an one-off app made by a small team, or for fun, the trade-offs may be worth it. But for Slack, or Skype for Linux, or VS Code, wouldn't it make sense to put more developer time on it and have a much more performance-conscious application?