Actually the show holds up pretty well for the most part. Seasons 3-5 in particular.
It’s after Fight the Future that things started to go off the rails, particularly with seasons 7, 9, IWTB, and the revival.
Season 8 is a surprising breath of fresh air though, so if you remember hating it at the time because of the Duchovny stuff, it’s worth a revisit. And the finale works very well as a series ending IMO.
Season 9 is just as bad as you remember, though.