As things are looking right now, I think we are already seeing Hurley take over for Jacob. His role has been to basically speak for Jacob and do what he would do. I know Hurley is the only person who can see him right now, but going on the "everything happens for a reason" bit, maybe this is what Jacob wanted. He knew he'd die and that Hurley would be the only person able to see/speak with him. So now, he is training him, telling Hurley how he decides things (like in Lighthouse, explaining why he needed Jack to figure it out himself instead of just telling him). This could also be a loophole of his own. He said he didn't want to interfere with people's decisions because that would defeat the prupose of what he is trying to do. But maybe in death, this rule no longer applies, and he is able to have Hurley interfere for him. This rule bending is similar to the killing of candidates (e.g. Dogen can't kill Sayid himself, but he can set it up so someone else kills him).
I think Jacob has to do with Isabella's appearance as well since it seems very coincidental that she suddenly shows up in Richard's time of need and tells him he needs to stop the MIB. Sounds an awful lot like a Jacob order, but Jacob knew it would mean more coming from Isabella.
Back to the point though, I think that in putting Hurley on these little missions, Hurley is already acting as if he were Jacob's replacement. He just hasn't been told that explicitly yet. Any thoughts?