I agree with your last sentence - Jake was really underused in the last few years of the show, and it was a real shame becuase episodes that focussed on him were usually dynamite.
I love ...Nor the Battle very much. It's a very visceral, traumatic experience for Jake to go through, and I thought it was portrayed very well. I think it's done slightly better in season seven with AR-558 and It's Only A Paper Moon, but by then the writers were taking more risks with open-ended episodes. It's a shame that Jake couldn't have a leg blown off or something. Anything, really, to help with his lack of development.