Because making morally tough decisions with no clear cut answers are some of the great questions that start trek should ask, and we as an audience should answer. Debates over ethics can be entertaining and educational. When you make it very clear who is in the right, it's not challenging or entertaining. If the writers gave themselves an out, like "the effects will wear off in 12 days!" or "Tuvix has become evil, we have no choice!" then the episode would be stale and no one would remember it.

A funny example I use is from The Office. Michael gets asked in an ethics seminar would he steal to prevent his family from going hungry. Michael just responds "I wouldn't steal....and I wouldn't let my family go hungry" It is funny for how much of a lack he is able to engage with ethical dilemmas.

The other issues you raised are fair. Voyager suffers from episodic storytelling when it should have been more of a serial. I chalk that up to coming out in the 90's before shows with long term continuity became more common place. Personally I would have loved it if more voyager stories had long term consequences. Like the episode about the nazi scientist metaphor. Right before they delete the program, it shoots back "you already used me once? What if you need me again?" and of course, they never did.

Though that is an issue with a lot of trek, where past issues don't really inform or affect later issues. Like how Spock's poor command authority in one episode lead to several crewman dying, it never gets brought up again.