Allow us to fill in the blanks of the animorphs universe.

[Zacharychaos]

Keep in mind that we don't know the Gedd population on the Yeerk homeworld, and the Yeerks have proven them to be at least passable hosts. For all we know, letting the Yeerks have their own homeworld would be equivalent to letting ten thousand or a hundred thousand or a million hosted Yeerks loose on the galaxy at once. Considering that the Yeerk Empire was grown from just a handful of Gedd-hosted Yeerks originally, I'd think that would essentially spell the end for the Andalites.

Strong possibility. Those dastardly Gedds, always threatening intergalactic empires and such! 

Again, one can only speculate how a million Gedds would invite an overpowering Andalite fleet but 5 billion physically superior humans? <Meh.>

[Salad Shooter]

1) Why, after infesting Alloran and 'sharing' the Time Matrix with Loren/Elfangor, why did Esplin 9466/Visser Three attempt to send the trio to the Yeerk home world?

My immediate response to this was that we know where Esplin 9466 intended to go, but not when.
It's possible he wanted to use the Time matrix to travel to just before the Andalites came to the Yeerk homeworld in order to get the jump on the first landing party. Scouting party lands on Yeerk homeworld, returns as controllers, and begins the secret invasion of the Andalite race without the Andalites ever even knowing what a Yeerk is or what to look out for.
With the Andalites as the first infested race, the rest would just be a domino effect.

A pretty reasonable explanation and one I (duh) didn't think too hard about. But then there's a whole other issue when it comes to attempting a secret invasion of andalites. Specifically, under what conditions would the sub-Visser be able to leave Alloran to feed for the first time, without Alloran thought-screaming about the threat? Unlike a human, being bound would be inadequate. It would be incredibly difficult starting from 1 andalite to successfully infiltrate others, because every single time an andalite-Controller feeds, ever, they would have the potential to alarm their compatriots. They would have to be knocked out or drugged, which is probably not a viable plan for the sub-Visser if he arrived immediately prior to "Seerow's Kindness".

My headcanon (described in more detail in my fic Primary: the rise of Esplin 9466) is that the Yeerks briefly retook the home world between the Hork-Bajir Chronicles and the Andalite Chronicles, but the Andalites eventually wrested it back from them.

So Esplin was trying to go back in time, but to avert the recapture of the Andalite home world. Which would be long after Seerow.

Seems like a reasonable possibility (out of the few that seem plausible) although it would raise the question of why the Andalites would throw a fleet at a non-strategic target (the Yeerk home world) when the real bottleneck was the Yeerk host availability. In other words, why drop the HB homeworld and go after the Yeerk world instead?

Because by that point the Andalites had already used the Quantum virus on the Hork-Bajir world. Not many available hosts there anymore.

[Tim Bruening]

True, Erek generates his own Kandrona rays, which may hurt the micro-oragnism idea, lest they are in the creatures themselves

If Erek generates his own Kandrona rays, then he could have fed Tom's Yeerk during "The Conspiracy", when Tom had to go to a funeral for 4 days!

Does Erek feed dissident Yeerks?