Currently when copying and pasting HTML to a VisualEditor form, the links are stripped. As far as I'm aware, this is not a technical restrictiong but a social one: we usually don't want direct links in the body of Wikipedia article, and similar content pages.
Still, there are many other situations where keeping those links in pasted text is very useful, and having to create them manually again is very tediious, For instance, in discussions.
Maybe a first improvement to the current situation would be to keep stripping links in Main namespace, but preserve them in the rest of namespaces.
If there is a possibility to configure this, then maybe even some Wikimedia wikis would like to default to keep links also in Main. For instance, in mediawiki.org or Meta I have missed the stripped links quite often. Third party MediaWiki users might just want to preserve links always as well.