I have only used Manual since I moved up to a DSLR. I don't think I even know what the other modes do (Shutter, Aperture, & Program). I have shot RAW since day one, I have never even tried the video mode, or the scenes modes. I don't even know what U1 and U2 actually do. I just got a flash 4 days ago, but I am so scared of it, that it is still in the box (I did open it up long enough to put batteries in it).
I shoot in Manual because I know what is going on in the camera when I do. I shoot in RAW so that I can correct more of my mistakes in post. I have not tried the other modes, as I don't know what the camera is going to do. I am a big scaredy-cat!
As far as the Modes you are not missing anything. The flash is no problem so come into the light.
I pretty much shoot in Manual only for the shooting mode, well I do not use any of the Auto settings in the camera. I change every setting as needed for the shot, or for the effect I want from the scene/subject. I shoot Raw+Jpeg so I even mess with the picture controls, to tweak the saturation, the sharpness, and even the brightness and contrast. Once you learn what the settings do you can pretty much get what you want in camera. This means you can get away with no post work, or very minor tweaks.
Just say no to Auto. Friends do not let friends shoot Auto.