Hey Nathan.
Great questions. In order to answer this, I am going to have to back way up.
I just got my 5D MkII, but have not had time to experiment with it yet. It is supposed to suffer less from overheating issues than the 7D and/or T2i/550, but still has some. They make case-mod cooling units, but there can also be questions of condensation, which ruins the internal circuitry (and also voids the warranty 🙁
Even with an RC-6 remote control, one still has to ‘start-stop’, which not only puts a jump cut in your timeline, but also kills your interview (because you have to worry about timing the start/stop, rather than just focus on your interview).
HDV is always an option, but I don’t want to go back to tape. I think AVCHD is a way better option.
I don’t know your budget, but if it were me, I would get a Zoom H4N like Josh advised, and a Canon HF S11/21, making sure I had two SDHC card slots, because you don’t want to use the onboard memory, except as a failsafe. I had one SDHC card fail, and all I had to do was just replace the card, which is a lot better than having to stop the shoot and send the unit in to B&H for service.
One gets 2hrs 55mins recording per one 32GB Class 6 SDHC card on full quality. I don’t know how long of interviews you want to do, but I cannot imagine running an interview for longer than that without taking a break long enough to get a drink of water, and change the card/s.
If I could afford it I would also pop for a Convergent Designs Nano-Flash unit and capture the uncompressed signal off of the HDMI Out port (which is pre-compression).
https://www.bhphotovideo.com/c/product/600482-REG/Convergent_Design_NANOFLASH_nanoFlash_HD_SD_Recorder_Player_with.html
The glass on the HF S10/11/20/21 is excellent, and I think that will probably give the best bang for the buck; and maybe even one of the best pictures available until they come out with the new hybrid DSLR’s next year (at which time the Nano-Flash is still useful). With glass that good, I would recommend the B+W 58mm UV filter, rather than the cheaper Hoya (as why put a lousy contact lens on an eye that good?).
If I had $7k for two Nano Flash units with CF cards I would spring for it right now. That is the route I wanted to go; and the only reason I got the 5D MkII instead of two Nano Flash units to hang off of my two HF S10’s is because I needed a 16-35mm super-wide angle lens in order to get full-body shots at 7 feet to camera.
As far as shotguns, I don’t know how one mic will cover two people unless you are sitting very close together (which in this culture I would think would be uncomfortable). Either you would need two shotguns, or two lav mics either on XLR cable, or, say, on Shure SLX wireless body packs (which I would think would be a much better option). Be sure to get good mics. They make a difference. I would recommend a Countryman B3, if you can afford it. Be sure to get the component that matches to the wireless you use (i.e. Shure SLX).
I hope that helps.
Norman Willis
http://www.nazareneisrael.org