This is very good. Our current setup is kind of a legacy situation — new links and stuff tacked on without concern for the grander scheme of UX, which I can't blame anyone for but has led to kind of a mess today. This shears away a lot of that legacy stuff, and more importantly cuts down on redundancy. The lack of SCP series at the top will probably hurt a little in the short term but I think it's an acceptable change in the interest of more clearly defining the difference between the side and top bars. That said, a few notes:
I agree with CQB that the for new users collapsible is… weird. I don't think it's bad, or that we need to get rid of it or even take it out of a collapsible. I'm of the opinion it kind of blends in with a similarly-hued background and color, and that if we want it to stand out to new users as "click here", we could do that by drawing more attention to it. Color changes, whatever.
I think the Random section should be put between the Series and Stories. The Random buttons are, I'm told, used for a not-insignificant number of people as their primary discovery method. It was my primary discovery method before I joined the site — I think it's going to be more used and should be in a more immediately visible position given that we're changing its look (from the three separate Random X links rn) from what people are used to already.
I think you should swap the headers for the Stories and Discovery section. It feels kind of funky to me that the section marked stories links to the GoI hub, the contest archive, the canon hub, which I would say falls better into Discovery, and the section marked discovery links to Tales, Tales, and New Articles, which I would say are stories. Just my 2c.
These are, of course, minor quibbles in an otherwise excellent and sorely needed slimming-down of our navigation system. I will support it regardless of whether the above suggestions are implemented or not. \o/