In all honesty, the first season is overrated. It is not some sort of shining pinnacle of television some folks make it out to be.
Who said it had to be a "shining pinnacle of television"? It was just good. We don't need caviar 100% of the time, but no one wants to live on McDonald's, either. (At least, I hope not.)
The first season had its problems but the storytelling and themes were not among them. They were building up a complex, ambiguous universe, and humans had to answer the question, "Are the Taelons here to help us or hurt us?" The answer turned out to be "yes."

Then it was decided that the Taelons would be primarily bad guys, albeit not as bad as some badder guys. I hate it when a show has its subtlety and nuance stripped away just to make it appealing to mass audiences. Christopher noted that that's what happened to Andromeda, too. I recall some comments by Kevin Sorbo about Wolfe, how Wolfe is so smart and has this great imagination and tells such complex stories but nobody can understand them, can we please make it more accessible? And, well, Tribune agreed.
The '90s had a lot of sci-fi shows that had one good season and then got retooled into shit, if they made it to a second season at all. (RIP, Total Recall 2070.)