Janeway smooth talked Chakotay into keeping his people in line.Rebel Maquis absorbed into Starfleet crew with little more than a 'She's the boss' from Chak ?
Raw materials shortages while they have replicators and enough power to run recreational holodecks ?
Severe damage regularly disappeared by next episode ?
A LOT of spare shuttles and infinite torpedoes ?
Lack of recurring background cast (on a pretty small ship too).
Much of this could have been addressed and dealt with relatively easily, or treated in a more rational way without destroying the TOS stand alone 'planet of the week' ethos of the show.
That they didn't really bother or only paid lip service to doing so says a fair bit about the show.
They traded for dilithium and the holodecks were often used for simulations I doubt Paris's pool scenario was on every night.
You do understand its the 24th century and that materials science has advanced don't you. It's not hard for them to have the Specs for torpedoes/shuttles and use spare or traded materials to construct them.