You're probably right about bodies getting possessed by dead people being common in season 1, even though I don't recall correctly. It's definitely something that will continue popping up, but I don't think it happened as much later on. Funny you should say you like the mythology episodes more. I love both the monster and mythology episodes, but I find the monster episodes often more fun to watch, while mythology episodes are more expository. There are some really fantastic ones however, like Little Green Men which is one of my favorite episodes of the series.
And yeah, the Flukeman scared the shit out of me when I first saw it! Incredibly effective monster design, and a brilliant episode as a whole. Even though yes the nuclear excuse is a bit cliché.
Season 1 is very strong considering it's a debut season and charming in its own way, if only a bit more hit-and-miss than other seasons, meaning a few episodes which make you shake your head. But the second half is when it really kicks in (although Fire is highly recommended, and has one of the season's best guest stars).