As someone who's run a ton of forums, I disagree it's the source of suboptimal forum content quality. If I had forced real names and identities, I would have lost a significant amount of users and activity. And not just trolls and spammers either.
A lot of people like to keep identities separate. Any system that tries to remove the anonymity site of things will end up stifling quite a few people who worry about their personal information being misused or who don't want everyone to know about their every activity online. That's not a bad thing, especially not in a world where intelligence agencies want to spy on everything you do, you could lose your job because of some comments on Facebook or Twitter and being swatted is sadly quite common.
Not everyone wants their friends and family to know they're an active member on say, Donald Trump Fan Forums. Or that they're posted leaked content from an upcoming game, like quite a few people on 4chan or Reddit. Or that they're interested in setting up a Tor node.
As for markdown, yeah, your solution there is exactly the solution. A GUI for new users, a raw editing text box for pro users. It's like how a lot of forum editors switch between BB code/raw text and a WYSIWYG editor.
Plugin copying is a good thing here (because the features mentioned could be good in other scripts), but I'm just warning you'll need quite a bit more if you want to differentiate themself enough from competitors in the market (of which there are thousands).