Both moves have a lot more utility than the average player realizes; they're both really disruptive when used by a smart player. You can not only really disrupt weaker recoveries for no risk gimps, but pushing people around is a pretty powerful thing to do for stage control and stalling for time in doubles (your partner is really destroying one of the opponents; throwing a stream of water in front of the other one can be a good idea). FLUDD needed to be stronger since it was sluggish and didn't push all that hard, but the basic idea of the move is really fine. It's also interesting and unique; Mario is the only character in the game who consistently has access to something like this (remember: anything on PT that isn't on all three Pokemon isn't consistent access) so powerful or not it provides some unique to Mario angles to work with in gameplay.
To be honest, I just don't understand this complaint because it's not really even about whether FLUDD is good; Mario Tornado was a really awful special move. As an attack, it was pretty useless, and as far as recovery moves go, it was incredibly marginal given that it gained little distance and was really slow while leaving Mario poorly protected (translation: Mario using the Mario Tornado to recover was very easy to gimp). On top of being an objectively very bad move, it was really boring and generic; I see nothing whatsoever to like in Mario Tornado. I can only assume people look at how much worse Mario is in Brawl than in Melee and just assume that his new down special has anything to do with it, but it's more about the combination of his attack power nerf and his low range being a larger disadvantage in a slower paced game. Those issues can and should be fixed for Mario, but none of that is at odds with FLUDD remaining or even being improved which I feel is pretty clearly the right design decision for Mario's moveset.