With Jimmy, I think they're being prepared. DM isn't getting any younger and I think they're hedging their bets for the time when, for whatever reason, Ducky can't be around. So they're bringing Jimmy along and making sure we're ready for him.

As to why he was in the bullpen, I kinda figured it was mostly for the same reason Abby was. They were waiting for the team to return. I'd love to see more of the Tony - Jimmy friendship. While Tony has been mentoring McGee in being an agent, I get the feeling he's been mentoring Jimmy in an even more older brotherly way.