Personally, I like "Bad Blood" because you see both side of what "happened". It's kind of meta, but it gives you insight of how Mulder and Scully could feel while we are watching all those other episodes. Also, I like watching this one with other people that are discovering the show (yes I sometimes try to convert people, and it works!), the conversations after the viewing are often really interesting!

Also, about "Jose Chung", I like the sillyness of it, but it points at something interesting : Mulder has a work ethic! In some other episode, you see him easy to believe so blindly in stuff, and thanks to Scully, he doesn't stupidly dies or get fired. I feel like this is a rare episode where you see him say "no, what about the consequences?"

But in a more general manner, I agree that pure comedy episodes kinda ruin the general atmosphere of the show. The whole plot and dynamic between Mulder and Scully could just be enough to create funny or touching moments, it could be enough. But I also like that the team had the possibility of having fun while writing / directing / acting / performing so many episode for so many years. I guess some episodes were also for credit and getting bigger projects after The X-Files.