I think Applegate could have done better with Davud's return as well. There's also a part about the book where Jake's family, including Tom, goes somewhere for four days to a funeral. It was the PERFECT time to make a "rescue Tom" mission. All they had to do was grab Tom when he was close to his three day limit, and starve the Yeerk. The other Yeerks would have no suspicions about a Yeerk just dying after a four day trip away from the pool.
They didn't even attempt it, though. Not as far as I can remember.
This is all in addition to the last book, which I won't even go into. I've already explained myself in that regard.
As far as books I didn't like go, parts of the latest ones come to mind. Maybe a sparce few parts of some earlier books too, but none that I can think of at the moment.
Edit: I didn't really mind the Helmacrons. If your people were more or less immortal, you probably wouldn't fear death either. The memories of the fallen just go towards the survivors.