Perhaps its a case of looking at it in hindsight but I can't see TNG ever doing an episode with an ending like Tuvix.
Not the way Voyager did it, I think. It left it up in the air that Janeway might have intenionally
committed murder of an innocent being.
I don't think TNG would ever play a risk with Picard's character like that. Then again....
Kirk would have found a way to save all three of them.
Picard would ramble on about the ethical implications for about 25 minutes, sipping a lot of earl grey, and probably even find a way to invoke the prime directive in it. Which way the decision ultimately would go, I can't say. Probably perform the separation procedure but store the Tuvix consciousness on the holodeck first until a way can be found to give him a body or some such thing.
Sisko would have done the same as Janeway, but ending the episode with a speech in his private quarters:
" I think I can live with it... And if I had to do it all over again... I would. I'm sure about one thing – a guilty conscience is a small price to pay for the safety of the crew. So I will learn to live with it...Because I can live with it...I can live with it. Computer – erase that entire personal log."
Archer probably would just have remarked that ''They're dangerous, those transporters... but one day, we'll get it right". And then it would have been time to feed Porthos.
With Sisko, I can see him letting Tuvix make his own decision to stay, but reminds him that he's killing two people in the process. Then in drunken guilt, Tuvix stumbles into the transporter alone and does the reverse procedure.
With TNG, I think it could have happened like this; Picard gives a speech about individual freedoms and rights and Tuvix would ultimately agree and have ended up going back into the transporter HIMSELF.
Problem is, you can't sustain that for 7 years straight. If they can't get over themselves and learn to co-exist, they'd never survive.
At the time of Voyager, the Maquis had barely existed for 1 year.
This is the problem, having their disagreements be based around a political dispute that was now 75 years away would get silly after a while.
To be honest, though, rational or not, for 7 years straight- it might have made for interesting viewing. I'm not saying it's rational either, but the viewers very well may have enjoyed seeing the crew bump heads throughout the show, and yet still somehow make it out of the DQ.
We realize that on the ship, both sides would have put aside their differences. In this case, we're talking about just one episode. Both sides had their opinions, but a lot of the animosity or resentment might have been more on the Maquis side than Starfleet.
A lot of them probably had personal experiences with being forced to leave their colonies or with brutal Cardassian soldiers . Starfleet officers were living relatively comfortably in their homes or starships.
It may have started out by accident, but a debate starts, and everyone airs their resentments and opinions. It gets intense, emotional, politics and history comes up, and everyone (the fans) are talking about it.
I think it would be pretty realistic, but entertainment wise, a serious missed opportunity.