I'd consider myself a proud peddler of Ikuhara pills to unsuspecting innocents and I have to admit that even I found the first episode or two of Yuri Kuma Arashi just a tad bit inscrutable. This may very well turn out to be intentional, and you are absolutely right that Ikuni's signature works (all three of them) always reveal greater depths upon rewatch, but on first pass it stands in quite a contrast with the misleadingly simple and innocuous first episode of Utena or the immediately beautiful and appealing first episode of Penguin Drum.
That said, over the course of the three episodes I watched last night, the intriguing qualities and manic tone of the show began to take shape as something more definite and interesting. I'm not ready to call it something great yet, but I can imagine that fascinating depositions of his favorite themes and motifs - the nature of interpersonal love and its limits, the failures of adults in creating a suitable world to pass on to their children, the oppression and the struggles of societal outliers, self-determination, incest - will show up at some point, if they haven't already, and that's an exciting prospect whether the final outcome is flawed or whatnot.
On one, more obvious level, the show is clearly interested in saying something about the perception of homosexuality in Japan, with the bears serving as a metaphor for the alternately cute (yuri) and threatening (real lyfe) ways in which culture views them depending on circumstance, while the Judgemens (THE MENS) are tasked with judging lesbianism on whether it is suitably sexy and cool. This is why there's a stock yandere and a pervy opening and copious references to lilies, an otherwise unremarkable flower, but there's obviously gonna have to be some elaboration and expansion on this point over the course of twelve episodes. I will give it time to, ah, bloom as I sit over here trying to figure out what bullets and birds and spiral stairs (!!) are supposed to mean.
(You mention Psycho as a touchpoint for the show, but I had my own nerdy moment of realization when the confluence of a mysterious, high-ceilinged school with distinctive red walls and the chanting of words to a cacophonous soundtrack gave me Suspiria vibes. It turns out that I wasn't alone and this particular scene wasn't solitary; I just hadn't noticed it before. An impressionist horror film like Suspiria seems an odd choice for such a strong, if obscure, reference, although it is about a mysterious school with a predatory secret council and a penchance for murdering the new students.)
