I would make a couple of changes to the ending.
I'm not going to get into the "whether or not Rachel should have died" debate, but personally, I have more of a problem with the way she died rather than the fact that she did die. KA chose to kill her off, and that's fine. And her death scene is one of the best written scenes in the whole series. However. Rachel's heroic death is completely cheapened by what Erek did, and if you're going to kill a main character off at the last minute, do NOT have it happen for nothing. Rachel's mission was to a) create a diversion so the Blade Ship could be taken out, and b) save Tom if possible. None of that happened, and I think it was an unecessary defeat. We get that war is hell, but everything doesn't have to turn out so dismally for everyone who fought. I wouldn't make it so Rachel lived, but I'd make it so she was at least able to carry out her final mission successfully. Tom's Yeerks kill her, but the Blade Ship gets taken out.
Secondly, I would get rid of The One completely. Could have been a cool character, if introduced before the last ten pages of the last book. The way it got introduced, though, is crap. You don't start a new storyline in the last third of the series' final book and then just leave everybody hanging. So, instead of Ax getting assimilated or whatever, I'd have some other threat pop up. Maybe a pocket of rogue Yeerks that escaped Earth somehow and are trying to enslave a new planet. Ax comes to Earth and enlists Jake and the others, besides Cassie, to help fight it. They name their ship The Rachel and take off into the sunset. Anis still go out fighting, humanity was saved, and there's at least a bittersweet feeling, instead of a depressing, unfinished one.
I would not have Cassie go with the Anis, because Jake made a good point. She DID move on from the war. She was a peacemaker, not a warrior. And I'd still have them split up. As others have said, I think Jake was scarred by the war, and he and Cassie grew apart, especially from #50 on. After Earth was saved, they wouldn't have the war in common anymore, and I don't think their relationship would've survived.