Yea, from the video it looks like the flaps are not in the takeoff position. Then again its not the clearest video. But from what I have learned, there is a very loud alarm when take off thrust is applied and the aircraft is not in the proper take off configuration.
I watched a YouTube video by Max Afterburner about the flight. He looked at the takeoff video and noted that the 787 was taking a long time to get up to speed, that it used pretty much the entire 11,500 foot runway -- it appears the plane had a lot of issues getting the speed to takeoff, and once off the ground it went up very slowly to only about 600 feet, before falling again. He noted the flaps not being extended and thought perhaps they were extended to a 1, rather than the 15 they would normally be for a takeoff like this. If they were extended at all, even to just a 1, it would prevent the flap alarms from going off.
Some appear to think that perhaps that the pilots, rather than put the landing gear up, accidentally retracted the flaps -- something that is possible, particularly in a case where the flight crew is in a crisis, such as with this flight. At this point, the idea is that the plane started to stall from the lack of lift, which caused them to start dropping.
Of course, we also have the one message from the cockpit of engine failure, which causes any number of questions. It doesn't rule out the above scenario, as a lack/loss of lift could be interpreted as an engine failure. But it also adds to questions about issues with hydraulic issues, fuel delivery problems (such as the fuel pump not working), etc. It is worth noting that a single 787 engine should be enough to allow the plane to takeoff, so somehow both engines appear to have failed.
Also, from one of the cellphone recordings, listening to the sound of the plane, it sounds as if the RAT (Ram Air Turbine) may have been active -- which is why the thought they may have had a hydraulic failure, and reinforces the idea of a possible dual engine failure.
Both flight recorders have now been recovered, hopefully this will help provide investigators with the information they need to come to a relatively quick and accurate understanding of the causes.