The only thing I hated about F.L.U.D.D. was that it was a permanent powerup that was permanently equipped and it was always there. Imagine how Mario Bros. 3 would have been if Mario was grafted to the Tanuki suit throughout the whole entire game and there was never any way to take it off and it was the only powerup. That doesn't sound like very much fun, right? Everyone loves the Tanooki suit, though, but that's only because its a special thing that you had for limited times. If you get stuck with something permanently it isn't so special anymore.
ETA: Or imagine Super Mario World with Mario being stuck to Yoshi the entire game. No matter how much fun something might be, if you can't ever break free of it the appeal will eventually fade.