Johnny and the Dead by Terry Pratchett
Second book in the Johnny Maxwell trilogy changes nothing about my requests for some changes to the protagonist, but it's significantly smoother than the first, Only You Can Save Mankind. In this one Johnny goes from leading an alien race to safety to helping out the local dead in the town graveyard.
It has some good philosophical bits, a lack of Kirsty (that's not a good thing), and the usual cute interactions between Johnny and his friends, who are still twelve. It isn't until the next book coming up, Johnny and the Bomb, where they finally get to upgrade to thirteen and get seriously involved in the adventures besides thinking Johnny's a bit strange.
In Johnny and the Dead, Johnny starts seeing dead people, and then the dead people start realizing they can do a lot more than lay around waiting for judgement day. Wackiness ensues.
I'm actually halfway into the third and final book of the trilogy, which I thought I'd be done by now but grandparents came over and one must entertain ones grandparents or they start biting.