Haha, I watched both eps twice before the podcast. I stand by My Struggle as the better episode.
I actually had the opposite reaction to you - I liked it better the second time around. The first time my excitement was somewhat tempered because I didn't want to disappoint myself. That said, I still felt somewhat let down just like I did after IWTB. But I read a bunch of reviews, thought on it quite a lot, and ultimately came to reconcile that there was a huge difference between my lofty hopes and what the actual show actually always was. That said, the episode is certainly not perfect. It needed to be longer, or - what I'd have personally preferred - they'd had more confidence in the audience to pick up what was going on if they'd jumped into the middle where Mulder was already deep into his investigation which led him to this new direction for the mythology. I'm really excited for where they go with this, but extremely worried that My Struggle II will suffer from the same problem as the first. Avi has some impressive connections, so she knows a lot of what's to come and she's spoiled me on some of it - so I know what's coming. Finger's crossed they pull it off in 44 minutes.
Founder's Mutation was a good episode, but I think the popular consensus that it's an all time great is misguided. After the admittedly imperfect My Struggle, it is a solid standalone, but I think most of the praise it's getting is due to the fantasy sequences with William, and for the back-to-basics use of horror and too gross to watch imagery. Personally, my favorite aspect of the episode was that it did, in fact, tie into the mythology and the experimentation on humans by injecting them with alien DNA. In my mind, Kyle and Molly are successful results of the Super Solider 2.0 program.