Ebb/Flow is really easy and what I prefer for my system, but I am also running more than 1 plant at a time.
Since you will need to have two different areas for the mothers/veg and for flowering anyways, then you need to make sure they are mobile. If you put them in pots, you can just do ebb and flow and simply move the pot when it is time to flower. Then the problem is as you said, no ability to vary the nute levels to specific plants, so the tray idea is out. You could still do E/F but fill closed in pots instead, but that is too complicated.
For your application, and wanting to do hydro, I am going to stick with suggesting the DWC because each different pot is at whatever ppm you put in it, and the root masses are isolated as to not pass any pathogens from grow to grow. E/F limits that pathogen transfer through the seperate trays, you should do it with seperate bubblepots.
As far as DWC specifics, I cannot help much. I have seen them in big shared containers to 64oz plastic cups. Go check out the DWC forum for more help there.
There also is the soil option. Lots of people do it and love it, it is an unknown for me.