It's fine that you think this is entertaining science fiction, and are grafting perceptions of "competence" on characters in this show. I don't want to nitpic everything in your response, except for this:
>Academy standards are probably a lot lower than they used to be, the show, actually goes into this a couple times!
The explanation for this makes no sense. This is the 32nd century (allegedly). The amount of advanced technology one would need to understand to be functional in this environment is extreme.
As an aside, and maybe this is the best way to explain my aversion to this show, the ship design is awful and makes absolutely no sense. I forget which "tech the tech" explanation there was for this, but every starship in Academy is a) hideous because the warp nacelles just float out in space for some reason, and b) makes no sense canonically. Star Trek used to actually respect engineering. Academy says "nah, fuck it, it's all magic now".