I started watching the X Files years ago, catching an episode here, an episode there. And I have to say that most of the underlying conspiracy plot was lost to me as a result. Consequently, I rated the show as OK, but nothing special. Something to watch if you happened to turn the TV on and it was playing, but not something to actively seek out.
However, I recently acquired all 9 seasons and set about watching them, in order, from start to finish, at about a rate of an episode a day. I have to say it all makes a lot more sense now. The conspiracy theorie's "on-off is it-isn't it" nature makes for confusing twists and turns which is exactly what it is supposed to do.
I can't really say whether the earlier seasons are better than the later ones or not. When you watch that many episodes over a few months they all seem much the same in terms of quality. There are standout episodes just as there are the odd turkeys, but overall the quality is good and fairly consistent.
What most people don't get, I think, is that the show became less about the conspiracy theory and weirdness and more about Mulder and Scully as the seasons rolled by. Perhaps this was why it was such a shock when Mulder vanished at the end of season 7 and was replaced by Doggett and Reyes. I too, was inherently antagonistic towards them but, I am very glad to say, they do grow on you. But the two seasons they were in were not really enough for you to get to know them intimately, as you did Mulder and Scully.
The show was filled with memorable characters such as CSM and the Lone Gunmen. Special episodes gave you an insight into these recurring characters and how they came to be who they are. Indeed, the Gunmen got their own show, albeit only for a run of thirteen episodes (unlucky for them!). Other characters like Gibson Praise, The Alien Bountyhunter, Pusher, Tooms and Agent Harrison also recurred and were pleasant enough to watch whenever they were on screen. Old faithfuls, if you would.
I've become, from an indifferent beginning, a definite fan of the show. It was a shame to watch the final episode and think that it was over, but here's hoping they make a couple more movies. I think it's probably a foregone conclusion that they will, since the ending of the show was left wide open with unresolved issues. But maybe that's what was intended, that the ending be a non-happy one. Only time, and another movie (or series) will tell.