I would get rid of the whole Atlantis adventure for starters, and I wouldn't have let Aftran and David get killed off (while it's possible that neither of them "died" in the strictest sense, they were still killed off) but really I wouldn't want to change much other than to mask the pop culture refrencs a little better, I know they're there to make the books hip and relatable, some were fine but these days some are just plain archaic and they never made sense for kids who want to keep their identies secret but already give a ton of information about themselve away. Also I'd fix the continuity errors.
Dak: We Hork-Bajir don't know how to to be violent . . . but every few years we go to war . . . it's a confusing time for us. Then again you want confusing just ask Jake, he can "think speak" in human form.
Jake: I "think cry" myself to sleep at night.
Iniss 226: You're confused? Is two-two-six my rank or my birth order or both? We Yeerks dont seem to know for sure!
But while I wouldn't take out a whole lot of things I would expand more on some things, for example Rachel and Cassie are supposed to be best friends but to read the books they both seem to have a kind of very unfriendly disdain for one another, especially later on when honestly I don't consider them friends so much as comrades. I'd expand on their interactions together to show why, despite this disdain, they're best friends, for example. Maybe Schoolastic says "It's too long now!" I just say "We can cut out all the product placement and pop culture refrences, thereby shaving like ten pages!"
I would however keep going past book 54. Maybe I'd focus on Cassie and David (remember, I didn't let him get killed off) if everyone else is dead. I've long had it in my head how the series could have continued after 54, I think I mentioned it somewhere else so I won't mention it again (since detailing it again wouldn't be "on topic" in the least)
But in truth I think I'd much rather write a companion series told from the perspectives of the Yeerks, Visser Three of course because he's awesome, Aftran because there was a truck load of potential for that character that just got dumped out to sea, the Yeerk that gets into Tom's head (was he ever actually given a name?), Iniss because as far as we know he maintains a decent position for the entire war (Chapman may have been given to a different Yeerk though), maybe Taylor and Visser One could share the "off" slot (as Tobias and Ax did at first) so I don't have to deal with Taylor much and can bring Visser One in as the occasional treat (her books don't even have to take place on earth, if we can see the Andalites plant a hork-bajir rebellion we can certainly see the battle for Anati) or else those could be given to say a Hork-Bajir controller and a Taxxon controller just to see more of the Yeerks and have characters who would actually fight the Animorphs face to face without the benefit of morphin to erase all their wounds. I'd love to write a book (well I guess I'm stuck with fan fiction) about a Taxxon controler dealing with the hunger, being almost the bottom rung of the Yeerk military, facing the Animorphs and coming out of it alive, he'd be a fun character to write for.