OK, you have to try this if you have not already:
In terms of focus, I think the X100 has improved quite a bit as the overall operation has gotten less laggy and has more snap to it. The AF hunts and misses less in medium low light, still misses in MF using the AF/AE-L button in the lowest of light though.
The biggest issue I see in manual focus is the larger AF box / target, it is just not anywhere near as accurate as when the camera is set on AF-S mode, especially now that decent parallax correction has been added on in the recent firmware upgrade. So I think that the way around this for Fuji would be to ditch the larger AF box version and just go with the smaller more accurate one in all modes, or at least have the option to. I almost never use the focus ring because it is simply too slow and not as precise as using the camera's AF system.
Often if you are photographing in situations that the subject is against or shot through a busy or bright background / foreground, the AF misses and either hits the background / forground it self or just lands on arbitrarily on 7 feet, regardless of what the subject or background distance is. However, it does *not* do this anywhere near as much when in AF-S mode with the far smaller and more accurate AF box, the hit ratio is much better.
So what I have done to combat this issue is either use AF/AE-L in manual when dealing with simply non-complex and darker than the subject backgrounds or use AF-S when the opposite, more problematic subject background combos are in play. The KEY to using it this way is to properly set up and use the combination of AF and lock buttons in this mode:
Simply go to the set up menu and set "AE/AF-LOCK MODE" to S and then right below it, set "AE/AF-LOCK BUTTON" to AF-L. What this allows you do to is simply lock the focus for as many shots as you want at where you hit focus until you either toggle the button off, review the image or shut the camera off again. Leave the button on and both the non-paralax corrected frame and the corrected one light up green and stay that way letting you know you are locked for as many shots as you like and then when you want to find a new focus point, hit the button again, nail focus and either lock it and recompose or just get one shot. This also works great in EVF mode for close ups.
With practice, I am finding this to be a great if not far better option to using the AF/AE-L button in manual mode.
Using the camera this way has made it a much more usable if not near perfect Leica-esque tool for me, I hope it does for you too...🙂
P.S., cut out two 4x4mm squares of gaffers tape and stack them on the Menu button. The difference in how well it works is amazing.