There are two sets of wires most likely because it's a dual voice coil sub, just like the 4th gens. If they haven't changed anything in the 5th gen sub, it's an 8" shallow mount sub (less than 4" deep), around 2.2 ohms, Dual voice coil (DVC).
There are lots of subs that will fit, but, the whole OEM amp & sub 2 ohm output thing really screws the pooch. You won't get much output from the OEM amp into an aftermarket sub. Your best bet if keeping it stock would be to tap the sub output from the amp, and connect an aftermarket amp to your new sub (speaker level inputs).
Brands, I would just keep it simple. The Pioneer shallow mount subs are actually very nice!