its kind of unfortunate that a lot of elements from the films will never be explained...
01 - the deacon bas reflief in the head room and the holograms
02 - the head in the head room
03 - the murals with the bird xeno + xeno hands holding the facehugger egg in the head room
04 - the deacon itself
05 - the scorpion ship
06 - exactly what happened between docking and the ship crashing
07 - 10 years of Shaw and David
08 - the engineers exact connection to the xeno
09 - is walter still alive
10 - what happens to the eggs left on the engineer planet
i could go on a bit more... but yeah, something tells me that the 3rd and final film will leave as many open and loose ends as the first 2 films did