Html5 wrapped export will never run as efficiently as a 'native' export, in the same way that a windows / virtual machine OSX will never run as quickly or smoothly on an i5 laptop as an installed version would.
You could probably say the same about hand-writing assembly vs. compiling code. Beyond a certain point, the difference doesn't matter any more.
I like to go with examples, so I'd like to get back to this quite old report also known as the "30fps cap"
No platform has all features. If we went with native engines, you'd probably lose support for browser-provided features like WebRTC, probably anything based on Web Workers (since they make multithreading so much easier to use), some service-backed features like speech recognition, probably user media features since they require a lot of cross-platform media support, you'd open the graphics driver bugs can of worms (browsers do a lot to sanitise WebGL), and so on.
Judging by the fact the 30 FPS cap feature only has ~30 stars despite the fact I always link to it, I think it's fair to say it's a niche feature. Everyone will always have their favourite feature they want which is difficult to do, regardless of the platform. For example users of native engines still want things like networking, including things like loading web-hosted images, which browsers do really well.
I'm sure someone will now say "but you could use libraries/frameworks to help", without realising the paradox that creates given others criticise us for depending on third-party code!