Well as a 5D MKII shooter, my scenes never have the need to go over 12 minutes so that's not really an issue. If I'm doing some sort of videography, I'll use a proper video camera, but for cinema where my scenes are only a few seconds to a minute and some change max, that limitation never bothered me.
As far as audio is concerned I use a 5.1 mic on cage and my recordist uses a separate recorder for the boom and shotgun. I only use the 5.1 for ambiance and since the AGC was killed in the big firmware upgrade in June the audio is flatly responsive and predictable. I know that there are XLR breakout cables or adapters that you can buy that have both input and output but I haven't fully investigated those.
One of the biggest reasons you'd want to use a rig like this is yes, it's only 1080p, but the sensor is HUGE for 1080p. Light gathering is amazing and the ability to not only get the depth of field of say a 1.2L lens but to also utilize the light gathering ability of a 1.2L lens rivals any adapter rig on a standard camera.
I do have one gripe though, monitoring through the HDMI port isn't 1080p it's 480p... if you play back from the camera to the monitor it's 1080 but it defeats the purpose of spending so much money on high resolution field monitors.
As far as auto focus is concerned, that's a feature used more by videographers imho. I have a RedRockMicro follow focus on my rig and it does fine for pulling focus in most scenes. I have my own hang ups with that but that's outside the scope of my post. :)
