I ran Serpent's Skull and the plot is a little forced at times, but the players and I had a pretty good time. I read through Strange Aeons and didn't find it compelling. If I ran it, I'd have to throw out about half of the plot, which eliminates the benefit of the AP for me.
By comparison, although I had to rewrite a lot of the encounters in Serpent's Skull as the game progressed, because the monsters as written didn't seem to be able to keep up with my players, the storyline worked, for the most part. There were a few hooks here and there that didn't hang together properly, but I wasn't left scrambling for an explanation or motivation too often.