I don't think Maynard ever lost interest in Tool, I suspect them suing someone because of the artwork and the insurance company suing them and another one suing another institution over and over for a decade or so had something to do with that.
Also disagree that FI is their nadir song-wise, imo Pneuma, Descending, Invincible & 7empest were worth the wait.
Prog metal songwriting takes time, and with compositions this complex, I expect them to. It's a wonder they play these songs live.