Despite its problems, I will always insist that Season 9 is just as good as past seasons, but in a very different way. There are a few stinkers, namely Lord of the Flies and Underneath, but despite being nine years old the creative team managed to come up with great episodes.
The likes of John Doe, 4-D, Improbable and Audrey Pauley are strikingly different to other X-Files episodes, and this approach should be applauded. Rather than complain that the show isn't what it was, surely people should welcome a fresh perspective on the X-Files? All four of these episodes, as well as Release, Hellbound, and Daemonicus compare very favourably with past episodes. William and Jump The Shark, although controversial, are good dramatic episodes. Scary Monsters is a pretty average episode, whilst Lord of the Flies and Underneath are plain terrible.
The mythology this season is a mixed bag. Nothing Important Happened Today I&II and Provenance/Providence were both written before the decision was made to end the show this year. As such, they offer few answers and raise more questions to fuel a potential myth arc for the next couple of seasons. As such, NIHT is pretty poor, and P/P are excellent episodes but serve little purpose. The Truth, the final episode, is great - but not as great as it could have been. It recaps the show's mythology, but relies too heavily on this. The final half-hour is as good as ever, with the final scene being the only imagineable way to end the series - with Mulder and Scully together.
There will be people who will never take Season 9 seriously, and I admit, it does seem to be something of an acquired taste. However, that won't stop me from singing its praises.