First, let me say that it's been at least five(5) years since I've last watched the series all the way through, perhaps even longer... and it was well before the second film ever came about. My memories of the show were mostly from watching the original broadcasts, as I think I really only watched my DVD's entirely once.
"So how did it stand up to time?" you ask. Quite well, actually. Even the earlier seasons with the horribly fuzzy video quality still stand up against most anything around now. The writing was strong from the start, and it stayed just as strong (if not stronger) through the entire series. The production was as incredible as technology really allowed and got better as new techniques were developed. Occasionally, early on, there were some iffy alien effects, one even being stop-motion if I recall correctly. That was a bit dumb... but in all, it holds up better than most anything else from the 90's.
I noticed very quickly that the ground-work for the entire mythology was laid out within the first few episodes of the first season. If they knew exactly what their plans were for the greater over-arcing story early on, then they did a fantastic job in setting it all up. If they didn't know until later, then they did an amazing job at tying in all the early stuff. Watching the series with the benefit of hindsight, the whole series flows and progresses just perfectly and flawlessly.
I don't care what anyone says, I HATE that damn blasted Cher episode. Worst of the whole series. I remembered detesting it back when it aired, and I hoped that maybe I'd find a new appreciation on my re-watch... but no. I think I hate it even more now than I did back then.
The first movie was pretty good, but I honestly have to say that I like the second one more. A lot of people complain about the post-series film because it wasn't big, explosive, or filled with aliens... but I think it was just perfect the way it was. I think most of the dissatisfied people just haven't watched the whole series in a long time and only remember that there were aliens, forgetting absolutely everything else that made the show what it was. The "focus" on aliens may have been what glued the show together, like mortar in a wall of bricks, but the essence of the show as a whole was more similar to the second film than the first... especially when the series is watched start to finish.
Many people also deride the last two(2) seasons because "Mulder wasn't in them" .... Actually, I've heard people claim that Mulder wasn't in the last three seasons. They are wrong. He was in every season up through the end of seven(7) and was in half (sporadically) of season eight(8). Even in the season 8 episodes Mulder wasn't in, his presence was constantly felt, as he was constantly being searched for or referenced. During season nine(9) however, he was gone... until the very end of course. In short, Mulder's absence from the series as a whole was very slight and minimal... and is very easy to get over when not watching week-to-week.
Due to Mulder's absence, fans also hated on Agent John Doggett. This had nothing whatsoever to do with the character or actor, aside from the simple fact that he wasn't Mulder. This is stupid. Not only did Agent Doggett fit very, very well within the X-Files universe, but I actually find it hard to think of him not being there. He was a great character that never once tried to actually replace Mulder. Hell, half the time Doggett was trying to find Mulder, and the other half was spent trying to come to terms with Mulder's work... but he wasn't a ringer, wasn't a tag-along, and wasn't a horrible character. He was however a fantastic and under-appreciated character of which fans need to re-assess their opinion.
Sein und Zeit and Closure (a two-parter) make up some of the best and most emotional hours of television I have ever seen. Pretty much the entire episode(s), I was choked up... and I'll admit I teared up quite a bit when Mulder embraced the ghost/spirit of his sister. That scene alone is heart-wrenching and comparable with the famous "I'll find you, Penny" scene from LOST (The Constant) on levels of pure emotional magnitude.
To finish up, I'd just like to state that they not only laid out the mythology very well, but they also closed it all up just as well. Even before Mulder's "disappearance", they perfectly tied up almost everything for his personal journey... leaving just enough open for the series ending. Even Agent Doggett's personal story was able to find his own sense of closure before the finale... and the "...but I'd like to know how Mulder and Scully fared after the end!" plea was brought to light with the somewhat unexpected film "I Want To Believe" seven(7) years later.
Well, that about wraps it up for my Re-Watch-A-Thon... soon, I will re-tackle Supernatural. But for now, I leave you with a short video montage of my favourite episode from The X-Files.