Ooh, how did I not know there was a thread for crazy Ani-theories!? I've got loads of 'em.
1. Mertil was originally female, but got fed up with Andalite sexism and went
nothlit as male so that s/he could attend the Andalite military academy. That's why s/he can't morph, and also explains the implied relationship between Mertil and Gafinilan.
2. Arbron could have demorphed, if he'd just lived long enough. The Living Hive (from TAC) is probably the adult stage of the Taxxon life-cycle, and the reason there are so few Hives is because not many Taxxons are able to live that long without being cannibalized. But, if that's true, then the natural metamorphosis process would have re-set Arbron's two-hour limit, allowing him to demorph. Because, yanno, he wasn't a tragic enough character as it was. :'(
3. The Iskoort homeworld is actually the same planet that was once called Ket, back in the Ellimist Chronicles. Both were/are riddled with inhospitable sulfur swamps, forcing the natives to live high above the planet's actual surface (crystals for Ket, seuss-towers for the Iskoort). The Ketrans were exterminated billions of years ago, but their planet was left intact, so it wouldn't be out of the question for another race to take up residence there. Finally, this explains why the Ellimist took such an interest in saving the Iskoort when he knew that the Yeerks wouldn't meet them for at least a few thousand more years, if ever. He wasn't saving the species, he was saving his old homeworld.
4. When you morph something larger than yourself, anti-matter is extruded into z-space.
5. The Time Matrix is actually a piece of whatever-dimension-the-Ellimist-lives-in, that had to be extruded when the Ellimist entered that dimension, as a way of preserving the law of conservation of mass.
6. Everything about the Helmacrons, from their apparent insanity to their utterly bizarre reactions towards the concept of death, can be explained by the fact that their consciousnesses are passed to other members of the species when they die (a passing remark made by Visser Three at the end of #24). They've learned everything they know about this whole 'death' thing by trying to figure it out from other species, and they still just don't quite get it, since they themselves don't actually die. Thus they kill and then revere their 'dead' leaders, make trivial decisions by murdering each other, and have no fear of death at the hands of much larger species. Yet they change their opinions of people who are living ("Those cowardly scumbags!") vs. dead ("Those brave soldiers!") in a sort of exaggerated-mock-version of what we death-fearing species do.
Pretty sure I have more, but I can't think of them right now.
That's sad. This whole war would have been avoided if the yeerks got the morphing power
I wouldn't be so sure. There's something to be said for preservation of identity and culture, and I don't think all Yeerks would have unanimously given that up, just because they could.
EDIT: Yep, thought of two more.
7. The Arn intended the Hork-bajir to eventually go extinct. Based on the timeline of the books, I calculated a rough estimate for a Hork-bajir lifespan, and it works out to about fifteen to twenty years (thirty, at the absolute most). However, as is mentioned several times throughout the series, Hork-bajir breed very slowly. Short lifespans and slow reproduction seem like an odd combination of traits for an artificial race, until you realize that the Arn only needed the Hork-bajir to stick around until the tree populations were healthy again, and then the Arn wouldn't need them anymore.
8. Andalite skeletons are quartz-based. For comparison, terrestrial animal bone is composed of a calcium-rich mineral called apatite, which is a 6 on the Mohs scale of hardness, where quartz is a 7. This is why Andalite tail blades can slice through terrestrial bone. Quartz is also slightly lighter than apatite, contributing to the Andalites' speed and agility.