I think complexity is a good thing in a show directed at children. Gargoyles was a VERY complex show, for instance.
Here's how I'd do it.
1. For the most part, NOTHING would be changed. I think Cassie did the right thing trying to find a peaceful solution to the war and it fits her character. I loved what Jake said in the Departure (which is my favorite book in the series)
2. Each episode would be an hour long. half hour is too short and would make things sped up too much, which was a problem I had with the tv show
3. The megamorphs would be 2 hour movies.
4. My ending would be somewhat different from the books:
a. Jake and Cassie WOULD get married. I hated that. Come on, what's wrong with a little romance in kid's stories? It worked in Harry Potter. They'd even have children, one of whom would be an estreen, just like mommy. And they'd go to Andal for a honeymoon, as you call it (I like it. "Andalite homeworld" was kinda silly.
b. Tobias and Rachel (who doesn't die. I mean, just because she wasn't supposed to join doesn't mean she's expendable) would get married. Tobias would return to his humanity realizing he has no reason to fight anymore and deserves some happiness.
c. No cliffhanger ending with The One.
5. I'd include the chronicles as straight to DVD stuff