Lifep04 batteries have cell voltages of 3.2-3.3 volt per cell, so it all depends on how many cells you have in a pack. e.g. 4-cells would give you 12.8-13.2 volts.
Brushless motors are smaller than brushed counterparts and a bit more efficient. However their low speed running is inferior to brushed motors and you will likely need to fashion some mounts to fit them in.
Brushless motors and controllers are available cheaply from Hobbyking.
Good links for hybrid systems. There's not much published on them. A good choice for the water pump is a peristaltic model, as they don't need check valves. The slower pumping speed isn't an inconvenience for a trim tank, as most of the time you'll be filling and emptying the main tank.
I'm not sure what the overall displacement of the a U47 is, but will take a guess at about 7-8 litres, which will mean your trim tank should be sized at about 100ml. That will give you the 1% you need to adjust for different water densities, plus a few grams more to create some downthrust for static diving.
Ebay is good source for cheap peristaltic pumps e.g.
http://www.ebay.co.uk/itm/NEW-DC-12V-Dosing-Pump-Peristaltic-dosing-Head-For-Aquarium-Lab-Analytical-Water-/311134007908?pt=UK_Pet_Supplies_Fish&hash=item4871083264For your main ballast system, you have a choice to make, do you want an aspirated system, or a recirculating one. Both come with pros and cons.
An aspirated system takes up less space, but you need to be surfaced to empty the tank. A recirculating system will allow you to empty the tank when submerged, however you will have to consider where you are going to store the compressed air when you fill the tank.
Either of these approaches can be taken with air pumps or water pumps.