All this seems reasonable and agreeable.
I don't mind the "Travel the land to reconnect with your allies" prologue, but I agree it might be time to move on soon-ish.
I agree on both points of the world map and time. Setting, at least to me, is really important to understanding a story and all good stories should provide context to the locations and time frame they take place in. Doesn't have to be super elaborate, but I think it should at least be there. I took a screen shot of the world map at the start of the first game and used it to keep track of which candidate came from which city state and what their specialty was. It might be hard to keep up to date, but a world map with everyone's current/last known locations would be pretty cool if the cast is going to be sprinkled around the country-to-be.
Some space to hide spoilers.
I actually really like Josie. In the first game she's rather unassuming and blends into the background. This works with the "Don't trust the people closest to you" vibe near the end of the first game; she is the one you were not supposed to trust. The second game changes her personality a lot... but not really. The stark change is in how she's much more cagey and ruthless, both in her memories and with the Prince. That makes sense as she's the grand deceiver and she's dropped the pretense. However, before the reveal, she almost never revealed anything about herself and was rather reckless with her experiments, so she hasn't changed that much. Other than that, she's still Josie. She still loves alchemy and still supports and cares for the Prince in her own way. That way just isn't what we thought it was.
I can see why people don't like her, but she's a morally gray character who's trying to do good for the people she cares about even if she trends towards evil herself. She's the product of her time with the original Jenos. So long as the final reveals of her character and motives are good and worthwhile, I think she'll be fine and doesn't need to change.