To answer your questions:
1. Yes. Unless you are flying pretty high up and the Flight Planner says you should up it to 5 second intervals. It seems like for most work 3 seconds would be great, but you have to choose the faster option to get your overlap right.
You can do whatever you want if you have the flattening lens. That is why its there. Go ahead and do full resolution. But, if you aren't using a camera with a modified lens, you have to do the 5MP. It essentially just crops out most of the image and keeps the center 40% or so.
Good question. We have never noticed that. But it doesn't really matter because you have to do timelapse!
We have been thinking about that. To be honest, as long as you start with a fully charged battery, the only power that is being used by the camera is the power it needs to operate, not charging, which is pretty low. We have found that with similar weight, it affects the actual flight time a statistically unmeasurable amount.
It depends what Flight Controller are using. Your Phantom 2 has basic Naza controller that can hold 16 way points, enough for 8 passes. People have installed WooKong flight controllers to get up to 50 waypoints, but for mapping purposes, you probably only have enough battery to do 8 passes anyway...
We are aware that our documentation is a little thin. We are working on a start to finish write that is very descriptive of both the theory behind the mapping process and the data collection itself. In the meantime, feel free to ask your questions here.
We haven't seen ProTune hurt any imagery, but it is a bunch of extra processing and we generally like to deal in the raw image if possible. I don't even know that it does much for still images.