The whole separating the child from the mother is turned in the first episode, and that tension creates character motivation in both the child and the captain who carries it out. Who admits on screen later that episode that it was a huge mistake and it’s why she leaves Starfleet for 20 years. At the period in time that the separation happens the federation has pretty much fallen apart because of the burn (due to some unexplained physics phenomenon warp technology failed over a hundred years earlier). So yeah it may seem like the federation was a utopia by our standards, but it was really a demonstration of a cooperative rather than competitive future (Communism v. Capitalism). And even in that future nothing is perfect, shit happens, you have to deal with it and do the hard work of building strong community.
One of the most central lessons of the whole franchise is sumed up in the kobyoshi maru, a test from the 22-2300s era of trek that is a literal unwinnable scenario. The lesson: it possible to make no mistakes and still lose. Pick yourself up and do your best.
Academy is about building back those ideals, structures, treaties, etc. that made ST feel like a utopia. It takes work to over come the prejudices, animosity, and bad habits of generational trauma and backwards thinking. Regardless of whether the show ends up being good, I can’t think of many messages that we today need to see demonstrated more clearly.
Episodes 4 and 5 of Academy are the best so far (5 is most current at time of writing).