So after being initially really discouraged by the new mission system, I've now played through all the content on VN+freeroam mode, and loved it. With renewed enthusiasm I'm having another go now at trying to work out the missions on full experience mode and I've had a bit more success (not much) by following some hints that someone posted a few pages back, but I stand by my earlier comments: the learning curve is far too steep and the mechanics too unclear. I think the risk is that someone coming to the game cold (who doesn't know how fantastic the story is) will just be mightily put off by the mission mechanics and throw in the towel, which would be a real loss.
Unless I'm missing something there's no way of telling what stats you need before you start a mission so it's trial and error to get a high enough level to pass. It's also not really clear to me how you raise certain stats such as charisma, since they seem to be linked to the interactions in the main story - yet to progress with these you need money from the missions, so it's a bit of a circle. I fully admit I haven't spent enough time really trying to understand the whole thing, and I don't doubt there is an optimum sequence that you're supposed to follow from main story to free roam interactions to missions, in order to have enough money at the right moments to be able to progress, but again it's really not obvious. A detailed mission strategy walkthrough is needed, I think, but should that really be necessary?