Negatives:
You need at least two batteries and they charge slowly. I avoid dirt cheap non-Fuji copies and try to find the Fuji's on sale. Others apparently use the least expensive batteries they can find and never have issues.
There is a learning curve. There are two finder modes and three AF modes. The focus area regions respond differently in different modes. Still, you can achieve just about anything you need to, but you have to figure out how to do it. Using just one mode of operation for every situation can cause frustration. You are knowledgable about parallax error and focus and recompose, so you should be in good shape. Read the manual and read the various free on-line user guides, but be sure that you read is relevant to the newest firmware. Turning on the audible focus confirmation beeps can help you learn how to get the most out of the AF. You can turn this off later of course.
True manual focus (as opposed to operating the AF manually) is much more viable now, but it is nothing like using an analog lens. I find MF useful for checking and making adjustments using the digital zoom method. This is more flexible with the X100 than the XP and XE bodies.
The lens can create distracting flare artifacts when strong, point-source lights are present in high contrast situations. This is most commonly seen in night photography. The only defense is to reduce exposure but this only reduces the flare. The flare seems to be highly angle dependent, so not every light gives flare.
Lens filters are more likely to generate different flare artifacts compared to other digital cameras. The lens-sensor distance is extremely narrow which creates the reflections. Even high-quality filters with excellent coatings can cause problems.
The lens is not designed for close up work at apertures openings larger than f 4. So in macro mode you have a f 4 lens.
The live histogram display is essentially useless. Of course you already know how to expose and the histogram can be turned off.
Speaking of exposure, the highlight recovery in raw files is impressive. When in doubt overexpose. I believe bracketing exposures is good insurance.
Auto ISO is inflexible. Combined with auto DR strange things can happen (at least I find them strange).
The EC dial spins a bit too freely for some people. Newer bodies may have stiffer dials because the whining about this seems to have declined.
It is not convenient to change the shutter speed in 1/3 stops. Of course you are already use cameras that don't do this at all.
The in-lens ND filter is required in very bright light. This is annoying unless you shoot in bright light often. The camera will still operate when the shutter is too fast for the lens' aperture mechanism so you won't necessarily know the photos will have artifacts.
I wrote down every negative I could think of. Except for the point-source light flare, none of thes negatives detract from how much I enjoy the X100 every time I use it. Right now it is my default goes-with-me-wherever-I-go camera. Even before the first firmware update, I was thrilled Fuji made this camera.
