When Ax is in human morph, he goes nuts over food. Does Visser 3 have the same problem when he's in human morph? Does he direct his minions to be on the lookout for humans going nuts over food?
Visser 3 has no reason to eat anything in human morph. He didn't seem to use it much anyway. Also, the Yeerks don't have any reason to believe that the "Andalite bandits" would morph human. The only reason Ax did in the first place was because he had to work with his human allies.
The Animorphs keep saying at the start of the narrations that they can't give their last names or the name of their city for security reasons. However, they do give all their first names, the occupations of their parents, and the fact that Jake's brother Tom is a Human-Controller. Wouldn't that info be enough to tip off any Yeerks who happen to read their accounts?
I'm not sure why this is such a sticking point for people. The whole "writing down our accounts" thing is stupid. Even if the Animorphs concealed more details in these "accounts," the Yeerks would know anyway, because they would just be in the Animorph's room. It is just a stupid framing device that is used for the first 2 books until Tobias as a hawk in book 3 makes the whole thing void.
The Invasion: Why was Elfangor unable to morph? Granted, he was burned on half of his right side, but I have seen Animorphs demorph from far more serious injuries.
It's a plothole. KA probably didn't think about this kind of stuff when she was writing the first book. It seems to have taken a few books until she settled on the rules for these kind of things. Of course, you can always use the Ellimist argument.
The Visitor: The Chapmans both resist their Yeerks when their daughter is threatened. Why couldn't Jake resist his Yeerk at all during "The Capture"? Wouldn't he be at least as strongly motivated as the Chapmans?
Didn't he resist to some extent? This kind of stuff could vary on the strength of will between the Yeerk and human. Maybe Jake didn't possess the mental will that the Chapman's had, even though he would be as motivated as them.
The Capture: Ax emulates Jake for three days, and goes nuts over food. Why didn't that make Tom suspicious?
Again, I don't think the Yeerks would really be looking for this. Also, I don't think they understand the power of taste for an Andalite. Yeerks are just simply overwhelmed by all the senses, and probably can't relate to that.
The Alien: Ax pretends to be Jake's cousin Phillip, and goes to school. Shouldn't that make Tom suspicious, since he would know that Jake doesn't have a cousin named Phillip?
I thought Jake went to the middle school and Tom went to the high school.
Suggestions for Visser 3: Have his minions infiltrate the staffs of all food vendors so as to watch out for people going nuts over food.
See above.
Infiltrate the staffs of all animal handling facilities (such as "The Gardens" and "The Wildlife Rehabilitation Clinic" so as to catch Andalites trying to acquire new morphs. Cassie's parents would make excellent Controllers for that purpose!
Set up cameras all over town in hopes of catching "Andalite Bandits" in the act of morphing.
I don't think that's his style, but you could try helping him regain his sanity.
Suggestion for Animorphs: Have the free Hork Bajir (In existence from book 13 on forward) rescue Human-Controllers (including, of course, Jake's brother Tom, who would be a legitimate target due to his high rank).
I don't think the free Hork-Bajir think in these kind of terms. They don't see themselves as soldiers actively fighting the Yeerks, but rather as those who resisted being enslaved by them. The Animorphs have to respect their peaceful nature, and even if they tried to get them to fight, they would probably fail miserably. Hork-Bajir are kind of stupid.