I agree, the B plot was far more entertaining. It was a very "Lower Decks" plot in the vein of the original TNG episode to have Rutherford trying to figure out if he can fit into the other departments and to just deal with the day-to-day lives of a pair of friends dealing with mundane issues like conflicting work schedules. And the two of them feel like proper types you'd get at the low end of the Starfleet totem pole as the niche-interest keener and the excited "being a starfleet officer is a big adventure full of science and mystery and interesting stuff" newbie.
The other two stand out more and make it worse because they are basically contrary to the very idea that spawned this series. For as how that purports to be about the daily misadventures of the crew on the bottom rung of the command/operations structure of an unimportant ship (and therefore supposedly the least exposed to the most 'out there' aspects of space exploration and Trek life), for two episodes in a row Boimler and Mariner have gotten into crazy fantastic adventures that push out about as zany as they can get. Even the minor throwaway joke from the start of the episode with Mariner and Tendi encountering the energy being. In any normal Trek episode, encountering some "magical" wish-granting, reality-warping energy consciousness is a significant and plot-carrying thread that is treated like a big event. But just because they have to justify that these crew members are nobodies on a nothing ship, they treat it like a cheap meaningless gag so that Mariner can use the power selfishly for something bland like a new tricorder "with a purple stripe".
It makes it seem like the writers couldn't make it out of outlining their first draft of the pilot before they broke the mold of what the series concept was about, and they figured that since the show is animated they should use it to tell Family Guy/Rick & Morty style jokes that push things to their craziest because the medium has no restrictions like live action does.
A lower decks comedy should be like The Office or Parks & Recreation, but in Starfleet. Or the more "ordinary" parts of Futurama that use the potential of the future space setting to play up more "regular" issues for comedy. Instead we get WACKY WACKY WACKY WACKY starring over-the-top idiots.
And I agree that the two leads would probably not cut it in Starfleet outside of a comedy show. Well, maybe Boimler would as a forever-ensign who constantly believes he's capable of more than he is because his ambition outstrips his ability (think Rimmer in Red Dwarf), but I think we're supposed to believe that Mariner gets latitude and preferential treatment because her parents are an admiral and a captain and that the only reason she's even on the Cerritos is because it's her mother's ship. But there's no way that she should be able to get away with being as much of a don't-give-a-f*** troublemaker as she is without being drummed out of the service. And it makes her totally unsympathetic as a result (And no, a few seconds in each episode to try and show that she's doing it to be a good mentor to Boimler doesn't count)
At least not in the world before Michael Burnham made it OK to be convicted of mutiny that led to your captain being killed and then get back to command-level rank and responsibility within a year.