I think the problem isn't with reddit itself but more likely with the size of the groups trying to have discussion.
I want to just touch in your first point:
Reddit segregates people into distinct forums of people who all agree with each other, inducing them to engage in groupthink and shift towards increasingly extreme views.
My favorite subreddits have always been the really niche ones; fountain pens, pipe tobacco, coffee, midori, notebooks, urbansurvivalist, etc. And in these smaller communities I think a lot of good discussion happens within the purview of the sub.
Take fountain pens for example, while we might all agree that rollerballs are bad, few of us would agree on what the best nib size/material/design is. I have had the pleasure of reading over many civil and deep discussions over a wide variety of topics in that forum. Most of them are well reasoned and articulate.
It's when you get into the default subs that you lose all capacity for discussion. There you are just a single voice crying out to be heard in a sea of humanity.
If you only spent your time in the defaults of /r/all then you would never have a chance to speak. But in those smaller spaces real discussion can and does happen.