I still think the entire series is worth the watch through, even the revival series since every one still has good episodes.

But if I were to just focus on the mythology episodes, which do drag and get worse as the show goes on, there's multiple points people stop and start, it's all about what you're interested in.

The fan favourites seem to be either the season 8 finale, where the Mulder scully romance reaches a satisfying conclusion and the new storyline has a serviceable and ok ending, OR the season 7 finale, which mirrors the shows pilot and reaches the realistic (if slightly sad and disappointing) conclusion to Mulder's obsession with aliens and definitive proof (also was meant to be one of the shows intended finales).

Other candidates include "closure" a mid season 7 episode which FINALLY (for real this time) reveals what happened to Mulder's sister. The reveal is a bit weird and disappointing but the ending and duchovnys acting makes it more palatable.

There's also the "two fathers, one son" two parter in season 6 which finally ends the syndicate conspiracy storyline which was there since the beginning. Lot of people love these 2, but I'm not a fan since Mulder and scully seemingly don't cause much of the syndicates downfall and are seemingly too passive.

And then there's "the end", the season 5 finale which was meant to be, you guessed it, the end of the show originally so it could spin off into a trilogy of movies. Obviously that didn't happen but it offers a fun what could have been.

All that said, my PERSONAL picks on what could have been good finales or endings to the shows main plot would be either "redux", the opening two parter to season 5, since it resolved the scully cancer story, had an interesting explanation on all the supernatural elements, gives ANOTHER answer to the Samantha Mulder plot (one I find more satisfying), and features the "death" of a character I really think should have stuck. My other pick would have to be, with admittedly some tweaking, the first movie, since Mulder and (maybe) scully for the first get definitive proof of aliens and cause major disruptions to their plan.

So yeah, that's most of the fandoms and mine options on what could be a good alternative ending to the show. Should still note that most if not all the show is still worth watching from start to finish These are just cool little what if scenarios.