If there is the facility to use a VCS on WP.org then even more reason to utilise it fully.
The main advantage of open source software is community collaboration and contributions, so this needs to be made as simple and quick a process as possible. If I've got an improved version of a plugin that other people would benefit from, or I've fixed a bug, then why not contribute it back, and it also means that I wouldn't lose my changes then the maintainer releases a new version. At the moment, there is no way to do that and I'm sure that plugins are losing contributions because of it. The best way that I think would be to submit a patch along with my support request that the maintainer can review and (hopefully) approve and commit.
Essentially, it's less work for the maintainer to do compared to just creating an issue outlining the problem or feature request, so I think that the number of contributions would increase.
I realise that GitHub is a way around this (I prefer Git to SVN) but there seem to me to be plugins on WP.net that aren't on GitHub and vice-versa. As a WordPress newbie, I need a definitive place to search for a plugin to do what I need.
I think that the way that plugins are managed and hosted and which VCS to use etc is part of a wider discussion, but I think that my suggestion would improve the system that's currently in place.