So I am going to run my group through JR now finally and I started reading through the campaign log, after the first mission do the heroes get to choose their next story mission? It doesn't say which one to play.

Yes. See RRG.

Missions said:

During each Mission Stage, the heroes choose one active mission to resolve.
-- The campaign log lists the type of active mission the heroes
can choose during each Mission Phase. For example, if it
says "Story Mission" the heroes must choose an active Story
Mission to resolve. There is often only one active Story Mission
at a time.

For flavor, it's kind of like the heroes are picking out contracts or bounties to follow for Jabba, rather than being appointed missions by Rebel high command.

Kind of a neat twist on the structure of campaign.

Ya I definitely like it, and all I give them to go on is what it says on the mission card right?

Yeah, they don't get a peek at the map or anything.

Just like when choosing between the available side missions (including threat and agenda side missions), by looking at the information on the mission cards.

And reward cards are open information, in case a mission card mentions one.

It's interesting that you get to pick, but the fact that the missions are wildly unbalanced sort of ruins it for future playthroughs. It makes more sense to do it the original way with the harder mission following a win and the easier one following a loss. Once you've played Jabba's Realm a couple times you know the path of least resistance and just play that.

3 hours ago, Union said:

It's interesting that you get to pick, but the fact that the missions are wildly unbalanced sort of ruins it for future playthroughs. It makes more sense to do it the original way with the harder mission following a win and the easier one following a loss. Once you've played Jabba's Realm a couple times you know the path of least resistance and just play that.

That's definitely an issue.

With any luck, different compositions of Rebel heroes facing different Imperial Classes and Agenda cards may make some difference to that (but not a lot I expect)