You mentioned that low-light and autofocus were your top priorities. For better low light performance, you need a larger sensor and faster lenses. Larger sensor and faster lenses means shallower depth of field, which means more difficult autofocus. Most of the large sensor cameras you mentioned use contrast-detect autofocus, and they will hunt if you run them on continuous autofocus. So everytime your subject moves out of focus, the camera's autofocus will try to focus farther and closer to see which one is better. That appears as a very annoying autofocus "pulse" in the footage. So the bad news is that there's no free lunch -- you can have great low light peformance or you can have great autofocus performance but you can't yet have both.
That being said, some choices are better than others. The best large sensor choice in your original list is the A99 for three reasons. Firstly, it has the largest sensor in the list which means the most light gathering ability and the best low light performance. Secondly, it natively mounts the best lenses -- the Sony alpha lenses are much better than the Sony NEX lenses, both in optical quality (eg., resolution, distortion, etc) and in light gathering ability (ie., fstop). Thirdly, it has the pellicle mirror natively which means that it can use both contrast detect and phase detect autofocus during videos so it will likely have the best autofocus (most accurate with least pulsing). I'd recommend the A99 over the VG900 because you will have to use the LA alpha mount adapter on the VG900 to get the best lenses but you will not get the same autofocus performance as the A99 with it's native alpha mount. The downsides are that all the large sensor cameras in your list use line skipping to downscale their sensors to 1080p, which means they all have color moire and other ugly artifacts and none of them records a full 1080 lines of resolution.
Of the other cameras in the list, the GH3 and AF100 are good choices because you get a largish sensor, good autofocus, and a wide selection of good lenses (fast and high resolution). The AF100 has the better form factor but the GH3 will have superior low light performance (much better sensor) and superior autofocus (much higher speed contrast detect autofocus with less pulsing.) The GH3 can also record internally with much higher bit rates.
Personally, I would stay away from the NEX cameras with the APS-C sensors because you will be stuck using inferior NEX lenses with inferior (low speed) contrast detect autofocus. The A99 with the appropriate lens will give you better low light performance AND better autofocus performance. The GH3 will give you comparable low light performance, higher resolution (no line skipping and higher bitrates), and much better autofocus performance.
There's also a lot to be said for the professional video cameras. They have smaller sensors (bad low light, good autofocus) but they also come with very fast zoom lenses (eg., f1.6) which greatly improves the low light performance.
The low risk approach is to use a professional video camera. They're designed for professionals who want to make movies, like yourself! The DSLRs are designed for hobbyists and professionals willing to tinker to save a buck. Being a professional is all about risk minimization. You want to produce a good product with the greatest possible certainty. That's what the professional video cameras are designed to do. Using a DSLR comes with too many risks, like a critical shot is completely out of focus or the autofocus is pulsing or the sound is borked when the groom says "I do" or whoops the bride's dress is covered with horrible color moire.
One final thought - if you're going to be handholding the video camera, I'd also include optical image stabilization as one of your top criterion. Nobody wants to look at shaky footage of their own wedding.
That being said, some choices are better than others. The best large sensor choice in your original list is the A99 for three reasons. Firstly, it has the largest sensor in the list which means the most light gathering ability and the best low light performance. Secondly, it natively mounts the best lenses -- the Sony alpha lenses are much better than the Sony NEX lenses, both in optical quality (eg., resolution, distortion, etc) and in light gathering ability (ie., fstop). Thirdly, it has the pellicle mirror natively which means that it can use both contrast detect and phase detect autofocus during videos so it will likely have the best autofocus (most accurate with least pulsing). I'd recommend the A99 over the VG900 because you will have to use the LA alpha mount adapter on the VG900 to get the best lenses but you will not get the same autofocus performance as the A99 with it's native alpha mount. The downsides are that all the large sensor cameras in your list use line skipping to downscale their sensors to 1080p, which means they all have color moire and other ugly artifacts and none of them records a full 1080 lines of resolution.
Of the other cameras in the list, the GH3 and AF100 are good choices because you get a largish sensor, good autofocus, and a wide selection of good lenses (fast and high resolution). The AF100 has the better form factor but the GH3 will have superior low light performance (much better sensor) and superior autofocus (much higher speed contrast detect autofocus with less pulsing.) The GH3 can also record internally with much higher bit rates.
Personally, I would stay away from the NEX cameras with the APS-C sensors because you will be stuck using inferior NEX lenses with inferior (low speed) contrast detect autofocus. The A99 with the appropriate lens will give you better low light performance AND better autofocus performance. The GH3 will give you comparable low light performance, higher resolution (no line skipping and higher bitrates), and much better autofocus performance.
There's also a lot to be said for the professional video cameras. They have smaller sensors (bad low light, good autofocus) but they also come with very fast zoom lenses (eg., f1.6) which greatly improves the low light performance.
The low risk approach is to use a professional video camera. They're designed for professionals who want to make movies, like yourself! The DSLRs are designed for hobbyists and professionals willing to tinker to save a buck. Being a professional is all about risk minimization. You want to produce a good product with the greatest possible certainty. That's what the professional video cameras are designed to do. Using a DSLR comes with too many risks, like a critical shot is completely out of focus or the autofocus is pulsing or the sound is borked when the groom says "I do" or whoops the bride's dress is covered with horrible color moire.
One final thought - if you're going to be handholding the video camera, I'd also include optical image stabilization as one of your top criterion. Nobody wants to look at shaky footage of their own wedding.