It would have been best if the last book was a Megamorphs book, but I think by that time Applegate was just ready for it to end. She didn't want to do another big Megamorph sized book.
I think #54 should have been two books, myself. The #54 we all know and have an ambivalent relationship with should've discussed the end of the Yeerk war, and then covered the first year after its end in much more depth. Then we would've had room to find out what happened to Loren, Eva, Peter, Chapman, Melissa, the auxiliaries (seriously, if they were all killed, as is probable, how come they didn't get any memorial and are never mentioned again? Jake doesn't feel guilty about them at all?) and anybody else you can think of. We could have 40 or 50 pages of that, instead of 5 pages of Marco going, "Yeah, here's what happened to the main characters and Arbron and Toby. And now, let me go on and on about how rich and famous I am!"
The final book, #55, could then cover the next two years. I also think a really cool and much better ending to the series would be everybody climbing aboard the
Rachel, and just leaving it there. As someone said on another thread (or maybe earlier in this one), we get into another story and then are just left hanging.