Yea, a lot of ideas are reprised throughout the album, but this isn't unlike Floyd anyway. Clouds has a bit of a halfbaked feeling, it doesn't flow like their other albums and a lot of the songs (while good) aren't fully fleshed out. Obviously this is understandable as this seemed like a quick project that isn't really a traditional Floyd album. I'm sure if they treated it like Meddle or DSOTM, it'd be just as great as those albums.
That said, I still like it a lot.