To drift away from the ending, something I would do differently had I wrote the series...
I would not have let Visser Three turn into a joke. The first books really gave you the scope of it. He's an alien warlord who can, at will, turn into some of the most lethal and brutal creatures in the galaxy, and has nothing on his mind but the completion of his goals. He was untouchable. His presence instilled fear, and it very well should. His voice sent chills down the Animorph's spine.
Yet, he decayed to a buffoon. With all his power and all his morphs, he was barely even registered as a threat to the Animorphs by the end. A creature, who through study, intelligence, and unconquerable will gained his position over the course of decades... is easily and consistently outsmarted by a handful of teenagers. That was what bothered me the most.
In all his power and (originally) intelligence, with all his lethal morphs, he is regarded as a joke by a handful on teenagers who can turn into things with sharp claws and teeth.
The grape juice, the oatmeal... I would not have set that up the way it was.
For what I would change... I would maintain Visser Three as the one who the Animorphs ran from at the mere sight of him. He would maintain his intelligence and status, and not be the ignoramus who could not create simple plans to capture six people. As is common with this many books, decay is unavoidable if the heroes are to survive and keep winning. Fine.
Put him in less books. One out of six, ten books, it doesn't matter. He needs to maintain his status. To replace his decay, give him a subordinate or two. Visser Five, Sub Visser Four; it doesn't matter. Let the other be the one, who, while seemingly intelligent, and also has some sort of power, that the Animorphs consistently defeat. Let another be the one to decay.
Visser Three needs to maintain his threat simply because there is no replacement. If you bring in Visser Two earlier, and make him a genius, make his plans, while few, infallible; it won't matter. He won't have the only Andalite Controller in the galaxy, who can morph into creatures that can kill anyone instantly without challenge, on a whim.