Tangentially, I’m watching “the wolf inside” rn and two things occur. Firstly, this one seems most like a DS9 episode to me - very reminiscent of the DS9 MU episodes (well, at least “crossover”). Secondly, the scene with Tilly, Saru, and Stamets in the lab is very good. I really like those three characters - they seem the most “Trek” like and tend to do Star Trek-y things - like science and that.
Given the mysterious red matter anomalies Pike mentions in the trailer for s2, I hope that the trifecta mentioned above are in more episodes.
Tilly is cleverer than Michael is stated to be. She figures out Stamets’ connection to the mycelial network and how to help him. She’s more endearing than Michael - for an “outsider” type character who has flaws etc - Tilly is much more relatable. Saru is also a natural for a science-y type problem, given his previous position as a science officer on the shenzhou. And Stamets is sort of a bio engineer so it’d make sense to have him involved in the study of the red swirlies.
Michael hasn’t shown any great aptitude for science things in DSC - she seemed more at home in the MU in command of a starship. Probably because she had all those years as XO of the shenzhou. Hopefully the roles of Tilly, Saru and Stamets will be larger in s2 - if anyone can work out what those red things are, they can.
With that in mind my guess would also be that the red things are an illness in the mycelial network -
possibly allowing the other universes from “parallels” to break through.
She did figure out the Tardigrade stuff.
And she figured out most of their secret project just from reading some code. Not to mention other less sciency moments in which she proved her intelligence, like distracting the Tardigrade, convincing the computer to save her life, tricking the Terrns, etc. I think Michael's reputation as an extremely intelligent officer has been reasonably well earned - it's just that the show moved her out of the science position after the tardigrade stuff was done, so everything she gets after that is just more general command stuff. But that probably won't last. I expect she'll officially be the Science Officer in season 2, so we'll see more of that side of her again.