I'll just copy the list I sent to my sister here:
[spoiler]XenoFrobe said the following:
Here are the books in the order you should read (or skip over) them:
1: The Invasion
2: The Visitor (Other people say skip, I say read. Sets up Rachel and Tobias nicely.)
3: The Encounter (One of Tobias' most badass moments in here)
4: The Message
5: The Predator
6: The Capture
7: The Stranger
Megamorphs 1: The Andalite's Gift (Skip this one. Just a rushed monster of the week episode.)
8: The Alien
9: The Secret (In which Cassie is a terrible person. Sets up her character for some weird decisions later. Optional.)
10: The Android (Real life fan who won a contest online got to be an insert character, and accidentally ended up becoming a major side character in the series because Applegate like him. XD)
11: The Forgotten (Just a stable time travel loop episode that hits the reset button. Skip.)
12: The Reaction (Optional. Rachel makes some dumb moves in here.)
13: The Change (Tobias book=good book)
14: The Unknown (ohgodnoskipskipskip)
15: The Escape
16: The Warning (Obligatory "internet is full of creeps" PSA episode, but it is AWESOME anyway.)
17: The Underground (Meh, filler. "Battles that involve oatmeal are just never going to end up being historic, you know?")
18: The Decision (Way cool episode. Aliens rule.)
Megamorphs 2: In the Time of Dinosaurs—(Creates some inconsistencies, but makes up for it with great character moments.)
19: The Departure (Great Cassie episode, mainly because it show what a horrible hypocrite she is.)
The Hork-Bajir Chronicles
20: The Discovery
21: The Threat ---------DAVID TRILOGY HOLY CARP
22: The Solution
The Andalite Chronicles (This one has the same plot twist as 23, so read in whichever order you want. I love the Doctor Who/Star Trek campy sci-fi feel of this one, though.)
23: The Pretender (Great Tobias episode.)
24: The Suspicion (Oh man the Helmacrons are annoying. Skip.)
AND THUSLY BEGINS THE ERA OF GHOSTWRITIA.
25: The Extreme (Optional filler episode, but has a potentially [unconfirmed] significant reference if you're trying to figure out some backstory much later.)
26: The Attack (Actually by Applegate, not a ghostwriter. One of my favorites.)
27: The Exposed
28: The Experiment (lol vegans. Applegate herself went in and changed the last chapter to have everyone eating hamburgers just to spite the ghostwriter, that's how bad it was.)
29: The Sickness (Cassie's greatest moment and episode here. She gets to be badass for once.)
Megamorphs 3: Elfangor's Secret (Time travel, hits the reset button, but does it well and HOLY CARP THIS IS BLOODY. Drives the whole anti-war theme of the series home as well as the finale, in some ways.)
30: The Reunion (PAYOFF)
31: The Conspiracy (Debatably skippable. It's an poor plot, but provides important context for later.)
32: The Separation (Worst possible Rachel episode. No.)
33: The Illusion (Pretty messed up episode. I like it.)
34: The Prophecy (Tie-in with Hork-Bajir Chronicles. Filler.)
35: The Proposal (Kinda goofy and dumb, but lays down some important plot for later and sets up for Visser. Applegate actually said this was one of her least favorites in the series, but it's still important.)
Visser (Basically The Yeerk Chronicles. Beginning of the Earth invasion. This is one of the books that makes you wonder how they got away with selling this to kids. Sex, drugs, alcohol, and brutal violence play pretty heavily in here, even if it's not all explicitly onscreen.)
36: The Mutation (Meh, filler.)
37: The Weakness (Some character stuff for Rachel.)
38: The Arrival (Interesting deconstruction of a Mary Sue character. More Andalites are always good.)
39: The Hidden (I like this one even though everyone else hates it, it's a good Cassie episode. I actually felt torn. Still filler though.)
40: The Other (Filler, and raises some questions, but introduces a new side to Ax. Also, more Andalites.)
Megamorphs 4: Back to Before (The obligatory 'It's a Wonderful Life' episode. Optional, but interesting and reveals something about Cassie.)
41: The Familiar (Skippable 'potential future' episode.)
42: The Journey (STUPID HELMACRONS NO GO AWAY)
43: The Test (It finally happens
)
44: The Unexpected (Filler, but not horrible filler. You get to pretend Cassie is a cool character for a little while. Skip it anyway, not worth the time.)
(The endgame begins here. Hoo boy, does it pick up.)
45: The Revelation (Several moments I was waiting for through the whole series, finally realized.
)
46: The Deception
47: The Resistance
48: The Return
49: The Diversion (Maybe the best Tobias book. So many emotional moments, and it highlights why I like him as a character.)
50: The Ultimate (Dang it, Cassie.)
51: The Absolute
52: The Sacrifice
53: The Answer
54: The Beginning (The reason I'm currently writing a fanfic. Depressing as all get-out. If you want a great ending, don't read Marco's last chapter and just pretend it never exists.)
The Ellimist Chronicles (GOOD GOSH THIS IS SO SAD WITH CONTEXT. Seriously, the last line alone is the most depressing thing I've ever read. The whole thing is like all the sad moments in Doctor Who all wrapped up in one book. If you want to read it during the main series, probably read it just before the endgame kicks in.[/spoiler]
You're actually both right. Jake shut the world out and didn't let anyone in until the trial. He resisted any attempts to get him out of his PTSD shell. Cassie was really put off when he finally admitted that he killed the Yeerks out of rage and revenge, which made her feel uncomfortable around him and led her to seek companionship elsewhere. They both just kind of grew apart from each other.